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Tumor tissue microorganisms are closely associated with tumor immune subtypes. Comput Biol Med 2023; 157:106774. [PMID: 36931204 DOI: 10.1016/j.compbiomed.2023.106774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/21/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
Studies have found that different immune subtypes are present in the same tumor. Different tumor subtypes have different tumor microenvironments (TME). This means that the efficacy of immunotherapy in actual applications will, therefore, have different results. Existing tumor immune subtype studies have mostly focused on immune cells, stromal cells, genes and molecules without considering the presence of microbes. Some studies have shown that microflora can strongly promote many gastrointestinal cancers. The microbiome has, therefore, become an important biomarker and regulatory factor of cancer progression and therapeutic responses. In addition, the presence of microflora can strongly regulate the host immune system, indirectly affecting tumor growth. Taken together, it is important to study the relationships that develop among tumor tissue microorganisms, tumor immune subtype, and the TME. In this study, correlations between microbial abundance, immune cell infiltration, immune gene expression and tumor immune subtype were studied. To accomplish this, tissue microorganisms and immune cell ratios with significant differences between the different cancers were obtained by comparing 203 gastric cancer and intestinal cancer samples. Two immune subtypes of intestinal samples were obtained by K-means clustering algorithm and tissue microorganisms, immune cell ratios and immune-related genes with significant differences between different immune subtypes were screened through Wilcoxon rank sum test. The results showed that Clostridioides difficile, Aspergillus fumigatus, Yarrowia lipolytica, and Fusarium pseudograminearum were all closely associated with the identified tumor immune subtypes. Our open-source software is freely available from GitHub at https://github.com/gutmicrobes/IMM-subtype.git.
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Şeyhoğlu E, Erden A, Kılıç L, Karadağ Ö, Akdağlı SA, Akdoğan A, Kalyoncu U. Pulmonary aspergillosis after treatment with infliximab in Still's disease and a literature review of Still's disease and pulmonary aspergillosis. Eur J Rheumatol 2018; 5:75-78. [PMID: 29657880 DOI: 10.5152/eurjrheum.2016.15081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The use of anti-tumor necrosis factor alpha (anti-TNF-α) agents has increased during the past decade in rheumatology practice. Opportunistic infections have been reported with anti-TNF-α agents in clinical trials and post-marketing usage. Aspergillus infection is a rare opportunistic infection that is associated with immunosuppression, and there are reported cases of pulmonary aspergillosis in various rheumatic diseases treated with anti-TNF-α agents. Here, we present the first case of pulmonary aspergillosis associated with infliximab treatment in a patient with Still's disease.
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Affiliation(s)
- Emrah Şeyhoğlu
- Department of Internal Medicine, Hacettepe University School of Medicine, Ankara, Turkey
| | - Abdülsamet Erden
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University School of Medicine, Ankara, Turkey
| | - Levent Kılıç
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University School of Medicine, Ankara, Turkey
| | - Ömer Karadağ
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University School of Medicine, Ankara, Turkey
| | - Sevtap Arıkan Akdağlı
- Department of Medical Microbiology, Hacettepe University School of Medicine, Ankara, Turkey
| | - Ali Akdoğan
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University School of Medicine, Ankara, Turkey
| | - Umut Kalyoncu
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University School of Medicine, Ankara, Turkey
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Calcineurin inhibitors impair neutrophil activity against Aspergillus fumigatus in allogeneic hematopoietic stem cell transplant recipients. J Allergy Clin Immunol 2016; 138:860-868. [DOI: 10.1016/j.jaci.2016.02.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/24/2015] [Accepted: 02/10/2016] [Indexed: 02/07/2023]
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Rosenberg LN, Peppercorn MA. Efficacy and safety of drugs for ulcerative colitis. Expert Opin Drug Saf 2010; 9:573-92. [DOI: 10.1517/14740331003639412] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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The use of infliximab for treatment of hospitalized patients with acute severe ulcerative colitis. CANADIAN JOURNAL OF GASTROENTEROLOGY = JOURNAL CANADIEN DE GASTROENTEROLOGIE 2009; 22:937-40. [PMID: 19018340 DOI: 10.1155/2008/749547] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND/AIM The use of infliximab in severe ulcerative colitis (UC) is established; however, its role in severe acute UC requires clarification. The present multicentre case series evaluated infliximab in hospitalized patients with steroid-refractory severe UC. METHODS Patients from six hospitals were retrospectively evaluated. Data collection included demographics, duration of disease and previous treatments. The primary end point was response to in-hospital infliximab; defined as discharge without colectomy. RESULTS Twenty-one patients (median age 26 years) were admitted between May 2006 and May 2008 with severe UC requiring intravenous steroids and given infliximab (median time to infusion eight days). Sixteen (76%) patients were discharged home without colectomy; three of these underwent colectomy at a later date. Of the remaining 13 patients (62%), all but two did not require further courses of steroids; six patients had infliximab as a bridge to azathioprine and seven patients were maintained on regular infliximab. Five patients required in-hospital colectomy after the initial infliximab. CONCLUSIONS In this real-life experience of infliximab in patients with steroid-refractory severe UC, infliximab appears to be a viable rescue therapy. The majority of patients were discharged without surgery and 62% maintained response either as a bridge to azathioprine or maintenance infliximab.
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García-López S, Gomollón-García F, Pérez-Gisbert J. Cyclosporine in the treatment of severe attack of ulcerative colitis: a systematic review. GASTROENTEROLOGIA Y HEPATOLOGIA 2006; 28:607-14. [PMID: 16373009 DOI: 10.1016/s0210-5705(05)71523-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Intravenous steroid therapy is the standard treatment in severe attacks of ulcerative colitis (UC), but 20% to 60% of patients fail to respond and require colectomy. Cyclosporine (CyA) has shown efficacy in steroid failures and could avoid surgery, but controversy remains. AIM The objective of this study was to conduct a systematic review to evaluate the effectiveness and safety of CyA in inducing remission in patients with a severe attack of UC. METHODS We did a systematic review using Cochrane methodology, including data from published (in English, French, Spanish or German) clinical trials done in adults using intravenous or oral CyA in UC. Data on efficacy are obtained from controlled and observational clinical trials, and for safety issues case reports are also considered. RESULTS 31 studies were identified which met the inclusion criteria, 22 (18 uncontrolled, 4 controlled) with intravenous CyA, and 9 (all uncontrolled) using oral CyA. Only 4 controlled trials (one in abstract form) are available, and only one compares CyA to placebo. However, efficacy results are very consistent in these 4 trials, and very similar to those in observational studies. CyA achieves remission in 91,4% and 71.4% of patients in controlled and uncontrolled studies using intravenous route, and in 71,2% using oral route. Two mg/kg/day seems so efficacious and safer as previous standard 4 mg/kg/day dose. Minor side effects are rather common but do not seriously limit therapy. Severe side effects, specially infections, are uncommon but clinically relevant with several deaths reported. CONCLUSION CyA (intravenous, 2 mg/kg/day) constitutes an efficacious and relatively safe alternative in the treatment of severe, steroid-refractory, attack of UC. To optimize treatment, the correct selection of patients, a standardized protocol and clinical surveillance are recommended.
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Affiliation(s)
- S García-López
- Servicio de Aparato Digestivo, Hospital Universitario Miguel Servet, Zaragoza, Spain.
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Abstract
Although colectomy for ulcerative colitis is curative, long-term quality of life is reduced. Intravenous ciclosporin 4 mg/kg/day has significant toxicity. There is now evidence that low-dose ciclosporin (2 mg/kg daily by intravenous infusion, or 5-6 mg/kg daily in a twice daily oral dosage) has an acceptable safety profile, even when used in combination with corticosteroids. Drug dosage should be adjusted to the levels of 150-250 ng/mL initially (random levels during intravenous infusion, or trough levels for oral use). Ciclosporin should be considered not only in those who have failed 7 days of corticosteroids, but also in fulminant colitis at day 3, if not responding to corticosteroids. The drug should be avoided in frail or elderly patients with significant comorbidity, and also where colectomy is likely to be necessary in the short to medium term. Ciclosporin should not be continued for more than 7 days, unless there is a definite response. A 70-80% initial response is likely, and responders are discharged on oral ciclosporin, adding thiopurines and tailing prednisolone rapidly. The drug should be continued for 3 months. The likelihood of avoiding colectomy over 2-3 years is 40-50%. More studies are needed to evaluate the use of oral ciclosporin in corticosteroid-refractory colitis in out-patients, and to assess whether monotherapy (without corticosteroids) is significantly safer, without loss of efficacy.
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Affiliation(s)
- D Durai
- Department of Medicine, University Hospital of Wales, Heath Park, Cardiff, UK
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de Saussure P, Soravia C, Morel P, Hadengue A. Low-dose oral microemulsion ciclosporin for severe, refractory ulcerative colitis. Aliment Pharmacol Ther 2005; 22:203-8. [PMID: 16091057 DOI: 10.1111/j.1365-2036.2005.02552.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The optimal modalities of treatment with oral microemulsion ciclosporin in patients with severe, steroid-refractory ulcerative colitis are uncertain. AIM To assess the applicability, in terms of efficacy and tolerability, of a standard oral microemulsion ciclosporin treatment protocol targeting relatively low blood ciclosporin concentrations, in patients with severe, steroid-resistant ulcerative colitis. PATIENTS AND METHODS Patients with a severe attack of ulcerative colitis and no satisfactory response to intravenous corticosteroids were started on oral microemulsion ciclosporin. Dosages were adapted according to a standard protocol, targeting a blood predose ciclosporin concentration (C0) of 100-200 ng/mL. Patients without a clinical response on day 8 were scheduled for colectomy. RESULTS Sixteen patients were enrolled. A clinical response was observed in 14/16 (88%). The mean clinical activity index scores and concentrations of C-reactive protein on days 0, 4 and 8 were 11.8, 6.7 and 4.1, and 50.3, 19.3 and 9.7 mg/L respectively. The mean C0 (days 0-8) was 149 pg/mL. The mean creatinine clearance rates on days 0 and 8 were 88 and 96 mL/min. One patient had an acute elevation of transaminases that resulted in discontinuing ciclosporin. CONCLUSIONS Even when dosed for a target C0 of 100-200 ng/mL, oral microemulsion ciclosporin for severe, steroid-refractory ulcerative colitis achieves an efficacy similar to that attained with higher, potentially more toxic levels. The oral route should replace intravenous treatment in this clinical setting.
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Affiliation(s)
- P de Saussure
- Department of Gastroenterology and Hepatology, Geneva University Hospital, Geneva, Switzerland.
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Benazzato L, D'Incà R, Grigoletto F, Perissinotto E, Medici V, Angriman I, Sturniolo GC. Prognosis of severe attacks in ulcerative colitis: effect of intensive medical treatment. Dig Liver Dis 2004; 36:461-6. [PMID: 15285525 DOI: 10.1016/j.dld.2003.12.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Severe attacks of ulcerative colitis have a high risk of colectomy. AIMS To evaluate the effects of standard medical management and to identify the clinical and laboratory variables capable of predicting the clinical outcome. MATERIALS AND METHODS Prospective study monitoring the clinical and laboratory variables in 67 patients with severe colitis. Therapy consisted of prednisone, cyclosporin if no response, and azathioprine for maintenance. End-points were colectomy or remission. Logistic regression analysis was applied for statistical evaluation. RESULTS Fourteen (20%) patients required colectomy, 34 (50%) patients achieved remission with steroids, 25 (37%) patients received cyclosporin, 19 (76%) with benefit. Increased body temperature, pulse rate, sedimentation rate and C-reactive protein levels on admission were significantly associated with colectomy. Sedimentation rate greater than 75 mm/h and body temperature exceeding 38 degrees C at admission had 4.6- and 8.8-fold increased risk of colectomy. Less than 40% reduction in the bowel movements within 5 days predicted no response to steroids. Azathioprine maintained remission in 70% of the patients. CONCLUSIONS Elevated sedimentation rate and fever at day 1 best predict colectomy in severe colitis. Less than 40% reduction in the bowel movements at day 5 predicts no response to steroids. Cyclosporin has a high rate of success in acute attacks and azathioprine in maintaining remission.
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Affiliation(s)
- L Benazzato
- Department of Surgical and Gastroenterological Sciences, University of Padua, Via Giustiniani 2, 35100 Padova, Italy
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Loftus CG, Egan LJ, Sandborn WJ. Cyclosporine, tacrolimus, and mycophenolate mofetil in the treatment of inflammatory bowel disease. Gastroenterol Clin North Am 2004; 33:141-69, vii. [PMID: 15177532 DOI: 10.1016/j.gtc.2004.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
In the past decade, immunosuppressive drugs have come to play an integral role in the treatment of patients with inflammatory bowel disease. Cyclosporine, microemulsion cyclosporine, tacrolimus, and mycophenolate mofetil can be considered for the treatment of patients with refractory inflammatory Crohn's disease, fistulizing Crohn's disease, and severe ulcerative colitis. This article reviews the use of cyclosporine, tacrolimus, and mycophenolate mofetil in patients with inflammatory bowel disease, with emphasis on pharmacology, results in controlled clinical trials, and safety, and issues related to dosing and toxicity monitoring.
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Affiliation(s)
- Conor G Loftus
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN 55905, USA
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Abstract
Intravenous ciclosporin 4 mg/kg daily is rapidly effective as a salvage therapy for patients with refractory colitis, who would otherwise face colectomy, but its use is controversial because of risk of toxicity, and long-term failure rate. Opportunistic infections remain a serious concern, with a number of reports of death related to ciclosporin. Renal and neurotoxicity are also well-recognized. The drug should not be continued for more than 3-6 months and its main role is as a bridge to azathioprine or 6-mercaptopurine. Risks of toxicity can be reduced by using lower doses (2 mg/kg/day intravenously), by oral microemulsion ciclosporin, or by monotherapy without corticosteroids. Preliminary evidence shows good response rates, but further studies are needed to confirm optimal use of this potent, but hazardous, therapy.
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Affiliation(s)
- A Barney Hawthorne
- Department of Medicine, University Hospital of Wales, Heath Park, Cardiff, UK.
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Pound MW, Drew RH, Perfect JR. Recent advances in the epidemiology, prevention, diagnosis, and treatment of fungal pneumonia. Curr Opin Infect Dis 2002; 15:183-94. [PMID: 11964921 DOI: 10.1097/00001432-200204000-00014] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Although pneumonia caused by fungi is not a common occurrence in the general population, disease in an enlarging immunocompromised population is encountered with increasing frequency. Fungal pneumonias are most frequently caused by Aspergillus spp., dimorphic fungi and Cryptococcus neoformans. Recent studies have identified risk factors of thrombocytopenia, environmental events (such as construction or renovation) and immunosuppressive drug therapies as being specific risk factors for invasive fungal disease in select patient populations. Diagnostic strategies to detect circulating antigens and polymerase chain reaction based detection systems have been explored to improve identification prior to the progressive advanced disease. Advances in prophylactic strategies include increased use of aerosolized formulations of amphotericin B, usually in conjunction with new and old systemic antifungal agents. Despite recent published guidelines for treatment of fungal pneumonia based on etiology, mortality remains high in some infections with advanced disease. Caspofungin, a new echinocandin antifungal, has recently been approved by the US Food and Drug Administration for the treatment of invasive Aspergillus infections in patients unresponsive to or unable to receive amphotericin B. A triazole antifungal, voriconazole, has shown promise in phase III clinical trials in patients with refractory fungal infections and is expected to be available in early 2002. Other echinocandin and triazole antifungals are under development in attempts to provide improved effective therapy for fungal pneumonia.
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Affiliation(s)
- Melanie W Pound
- Internal Medicine/Infectious Diseases/Academia, Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina 27710, USA.
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