Optimization of biologic therapy in children with inflammatory bowel disease (IBD) using modern biomarkers Abstract to thesis Study programme: Biochemistry and Pathobiochemistry Introduction: In adults, infliximab (IFX) levels correlate with disease activity and antibodies to IFX (ATIs) predict treatment failure. We aimed to determine the association of IFX levels and ATIs with disease activity in paediatric population. Methods: This study was performed as a prospective observational study. We prospectively collected blood, stool, and clinical data from 65 patients (age 10.5-15.1 years) with Crohn's disease (CD) before IFX administration, and measured IFX trough levels, ATIs, and faecal calprotectin levels (CPT). We used multivariate analysis to identify the predictors of IFX levels. IFX and ATIs levels were meassured using ELISA. Results: Lower levels of IFX were associated with ATIs positivity (OR [odds ratio] 0.027, CI [confidence interval] 0.009-0.077). Higher C-reactive protein (CRP) level, erythrocyte sedimentation rate (ESR) and CPT levels were found in patients with lower IFX levels. The optimal combination of specificity (50%) and sensitivity (74%) for disease activity was calculated for IFX levels ≥ 1.1 µg/ml using CRP level < 5 mg/l as a marker of laboratory remission. In a model that used CPT ≤...

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Inflammatory Bowel Disease (IBD) is a chronic and incurable condition that is increasing inprevalence across the globe. This illness consist of two forms: Crohn’s Disease (CD) andUlcerative Colitis (UC). CD is characterised by a patch inflammation pattern across the gut anda multitude of different factors, such as diet. Contemporary research has found a link betweengut dysbiosis and the development of IBD, suggesting that the microbial flora colonising the guthave a vital part to play in the development of CD.This paper aims to identify taxa associated with CD. This is done through the application ofmachine learning algorithms as standard univariate statistical methods fail to apply in the highlyinterdependent domain of the gut microbiome. The compositionally of the data and externalfactors influencing variance in the data will be taken into account.After applying a Center Log ratio transformation (CLR) to a MetaPhlAn3 taxonomic profile andusing a random forest classifier the following five taxa were identified as the most important inthe association to CD: Ruminococcaceae bacterium, Akkermansia muciniphila, Streptococcusparasanguinis, Flavonifractor plautii and Bifidobacterium bifidum.

Inflammation is often a protective reaction against harmful foreign agents. However, in many disease conditions, the mechanisms behind the inflammatory response are poorly understood. Often times, the inflammation causes adverse effects, such as joint pain, abdominal pain, fever, fatigue, and loss of appetite. Thus, many treatments aim to inhibit the inflammatory response in order to control adverse symptoms. Such treatments include TNFα inhibitors. However, a major risk associated with drugs inhibiting tumor necrosis factor alpha (TNFα) is serious infection, including tuberculosis (TB). Anti-TNFα therapy is used to treat patients with Crohn’s disease, for which the risk of tuberculosis may be even more concerning. Recent literature suggests Crohn’s might involve Mycobacterium avium subspecies paratuberculosis (MAP), an intracellular TB-like bacterium. This study seeks to investigate the risk of developing TB in patients with Crohn’s disease treated with TNFα inhibitors. A meta-analysis synthesized existing evidence. Evidence came from published randomized, double-masked, placebo-controlled trials of TNFα inhibitors for treatment of adult Crohn’s disease. Twenty-three trials were identified, including 5,669 patients. The risk of tuberculosis was significantly increased in anti-TNFα treated patients, with a risk difference of 0.028 (95% confidence interval [CI], 0.0011-0.055). The odds ratio was 4.85 (95% CI, 1.02-22.99) when all studies were included and 5.85 (95% CI, 1.13-30.38) when studies reporting zero tuberculosis cases were excluded. The risk of tuberculosis is increased in patients with Crohn’s disease treated with TNFα inhibitors. The medical community should be alerted about this risk and the potential for TNFα inhibitor usage favoring granulomatous infections and worsening the patient condition.

Bakgrund: Inflammatorisk tarmsjukdom innefattar både ulcerös kolit och Crohns sjukdom, vilka är kroniska inflammatoriska tarmsjukdomar. De båda sjukdomarna löper i skov med plötsliga försämringsperioder och långa perioder utan besvär. Det är viktigt att sjuksköterskan vidtar specifika omvårdnadsåtgärder samt förhåller sig personcentrerat där värden som värdighet bevaras för att stödja personen. Syfte: Att beskriva personers erfarenheter av att leva med inflammatorisk tarmsjukdom. Metod: Till metod valdes en litteraturöversikt och de databaser som användes var PubMed samt Cinahl Complete. Inklusionskriterier var vetenskapliga originalartiklar, genomgått peer-review, engelskt språk samt publicerade från år 2014 till 2024. Genom ett systematiskt urval arbetades tio artiklar fram, varav nio med kvalitativ design och en med mixad metod. Resultat: I litteraturöversiktens resultat framkom det att personer med inflammatorisk tarmsjukdom hade erfarenheten av att sjukdomen påverkade deras dagliga liv, både i det sociala livet och yrkeskarriären. Personer med inflammatorisk tarmsjukdom hade även erfarenheter att sjukdomen påverkade det emotionella välbefinnandet. Det lyftes även fram hur personer hanterade sjukdomen, vilka strategier som användes och stödets betydelse beskrevs. Slutsats: Litteraturöversikten visade att personer med inflammatorisk tarmsjukdom möter utmaningar inom många områden i livet. På grund av de anpassningar som individen måste genomgå är det viktigt att sjuksköterskan bidrar med stöd för att möjliggöra effektiv sjukdomshantering. Roys adaptionsteori kan ge sjuksköterskan en bättre förståelse för personernas anpassningsförmåga och kompensera med stöd för att hälsa och livskvalité ska upprätthållas. / Background: Inflammatory bowel disease encompasses both ulcerative colitis and Crohn's Disease, which are chronic inflammatory bowel diseases. Both diseases are characterized by periods of flare-ups with sudden exacerbations and long periods of remission. It is important for nurses to implement specific nursing interventions and to maintain a person-centered approach where values like dignity are preserved to support the person. Aim: To describe people's experiences of living with inflammatory bowel disease. Method: The chosen method was a literature review, with PubMed and CINAHL Complete as the selected databases. Inclusion criteria were scientific original articles that had undergone peer review, were in English, and were published from 2014 onwards. Through a systematic selection process, ten articles were identified, of which nine had a qualitative design and one used mixed methods. Results: In the results of the literature review, it was found that individuals with inflammatory bowel disease experienced the impact of the disease on their daily lives, including their social life and professional careers. They also reported that the disease affected their emotional well-being. Additionally, the review highlighted how individuals managed the disease, the strategies they used, and the significance of support. Conclusion: The literature review showed that individuals with inflammatory bowel disease face challenges in many areas of life. Due to the adaptations that the individual must undergo, it is important for nurses to provide support to enable effective disease management. Roy`s adaption theory can provide the nurse with a better understanding of individual`s adaptability and compensate with support to maintain health and quality of life.

Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic enteritis in ruminants, and has recently been linked to Crohn's disease in humans. To generate an effective vaccine against MAP, it is necessary to identify MAP antigens that trigger protective immunity. Unfortunately, not much is known about MAP proteins despite decades of research. We have previously shown that a 4.8 kb insert from MAP will produce a 16 kDa recombinant protein when expressed in Escherichia coli and 19 kDa recombinant protein when expressed in M smegmatis ( smeg 19K). The difference of 3 kDa in size of these expressed proteins may be related to posttranslational modificatjons that occur in Mycobacterium species. We hypothesized that smeg19K is a lipoglycoprotein since blast analysis revealed approximately 76 % amino acid identity between the MAP 19 kDa protein and a known lipoglycoprotein, the 19 kDa protein of M tuberculosis. This prediction was confirmed following positive staining of smeg19K with Sudan Black 4B, a postelectrophoresis dye used to stain for lipids. Smeg 19K has also stained positively for glycosylation with the lectin concavalin A, a highly specific stain for mannose residues. As expected, treatment with tunicamycin (an antibiotic known to inhibit N-glycosylation) and treatment with deglycosylation assay (non-specific for mannose ), showed no reduction in size of 19 kDa glycolipoproteins. Since covalent modification of proteins with acyl or glycosyl moieties alter immunogenicity and/or pathogenicity, the study here provides foundation for future experiments regarding the antigenicity of MAP 19 kDa lipoglycoprotein and its role in disease pathogenicity.

Tesis por compendio / [ES] La presente tesis doctoral titulada "Sistemas de liberacio'n controlada de fa'rmacos diseñados para mejorar el tratamiento de Enfermedad Inflamatoria Intestinal" se centra en el diseño, preparación, caracterización y evaluación in vivo de distintos sistemas de liberación controlada de fármacos en colon (CDDS, por sus siglas en inglés) utilizando como soporte micropartículas de silice mesoporosa, funcionalizadas con puertas moleculares. En conclusión, los estudios realizados demuestran que los materiales de silice mesoporosa, en combinación con puertas moleculares sensibles a estímulos específicos, tienen un gran potencial para el desarrollo de nuevos sistemas de liberación controlada de fármacos en el colon, dirigidos a mejorar el arsenal terapéutico disponible para el tratamiento de EII. La posibilidad de adaptar o personalizar la carga y las puertas moleculares hace que estos soportes de sílice mesoporosa sean una opción interesante para el desarrollo de nuevos sistemas de liberación controlada de fármacos en diferentes aplicaciones biomédicas. Finalmente, esperamos que los resultados obtenidos en esta tesis doctoral sirvan de inspiración para el desarrollo de sistemas de liberación controlada de fármacos innovadores y cada vez más inteligentes, para su aplicación tanto en medicina como en otras áreas. / [CA] La present tesi doctoral titulada "Sistemes d'alliberament controlat de farmacs dissenyats per a millorar el tractament de Malaltia Inflamatoria Intestinal" se centra en el disseny, preparacio, caracteritzacio i avaluacio in vivo de diferents sistemes d'alliberament controlat de farmacs en colon (*CDDS, per les seues sigles en angles) utilitzant com a suport microparticules de si'lice mesoporosa, funcionalitzades amb portes moleculars. En conclusio, els estudis realitzats demostren que els materials de si'lice mesoporosa, en combinacio amb portes moleculars sensibles a estimuls especifics, tenen un gran potencial per al desenvolupament de nous sistemes d'alliberament controlat de farmacs en el colon, dirigits a millorar l'arsenal terapeutic disponible per al tractament de MII. La possibilitat d'adaptar o personalitzar la carrega i les portes moleculars, fa que aquests suports de silice mesoporosa siguen una opcio interessant per al desenvolupament de nous sistemes d'alliberacio controlada de farmacs en diferents aplicacions biomediques. Finalment, esperem que els resultats obtinguts en aquesta tesi doctoral servisquen d'inspiracio per al desenvolupament de sistemes d'alliberament controlat de farmacs innovadors i cada vegada mes intel·ligents, per a la seua aplicacio tant en medicina com en altres arees. / [EN] This PhD thesis entitled "Smart drug delivery systems designed to improve Inflammatory Bowel Disease therapy" is focused on the design, synthesis, characterization and in vivo evaluation of several Colon Drug Delivery Systems (CDDS) using hybrid mesoporous silica microparticles as scaffolds containing molecular gates. In conclusion, the studies shown in this Thesis demonstrate that mesoporous silica materials in combination with responsive molecular gates have great potential in the design and preparation of new CDDS to improve the therapeutic options available for IBD. The possibility to adapt the cargo and the molecular gate makes mesoporous silica support especially appealing for similar controlled drug delivery applications in the biomedical field. We hope that the obtained results could inspire the development of new innovative smart drug delivery systems in this or other fields. / We thank the Spanish Government (projects MAT2015-64139-C4-1-R and AGL2015-70235-C2-2-R (MINECO/FEDER)) and the Generalitat Valenciana (project PROMETEOII/2014/047) for support. AHT thanks to the Spanish MEC for his FPU grant. We thank the Generalitat Valenciana (Project PROMETEO2018/024) / Hernández Teruel, A. (2019). Smart drug delivery systems designed to improve Inflammatory Bowel Disease therapy [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/129863 / Compendio

Inflammatory bowel disease (IBD) is associated with lifetime morbidity and the onset of disease frequently occurs in early life. Although IBD manifests throughout all ethnic groups, there has been marked heterogeneity in its incidence, prevalence, manifestation, and outcome. We sought to study the incidence, prevalence, and survival of ulcerative colitis (UC) and to examine the evolution and prognostic predictors of Crohn's disease (CD) and UC among Hong Kong Chinese. A total of 4 studies were performed to address these issues. One longitudinal cohort study examined the incidence, prevalence, survival and phenotypic changes of UC. Two other longitudinal cohort studies evaluated the phenotypic evolution of CD. One of them specifically compared the course of disease between patients with and patients without upper gastrointestinal tract phenotype. The final retrospective study identified clinical factors that predicted the occurrence of corticosteroid dependency and refractoriness in patients with IBD. The annual age-standardized incidence rate and point prevalence of UC per 100,000 Hong Kong Chinese in 2006 were 2.1 (95% CI: 1.1-3.7) and 26.5 (95% CI: 22.6-30.9), respectively. Incidence of UC has increased 6 times over the past two decades. The overall survival of UC patients was similar to the expected survival of the Hong Kong population. Phenotypic changes in CD also occurred in Chinese patients in the same way as the white patients with respect to disease behavior, though at a slower rate. Similar to the white CD patients, the location of disease remained relatively stable over the course of disease. Chinese CD patients had more upper gastrointestinal tract phenotype which predicted the need of surgery and subsequent hospitalization. On the other hand, the rate of proximal extension of UC was less than 25% after 10 years. In CD, thrombocytosis predicted, whereas colonic disease negatively predicted corticosteroid dependency. Stricturing CD was associated with corticosteroid refractoriness. In UC, thrombocytosis and extensive colitis predicted corticosteroid dependency, whereas anemia predicted corticosteroid-refractory disease. The results of these studies are important in the planning of health service and they also assist in the formulation of treatment strategy. / Chow, Kai Lai. / "May 2009." / Advisers: Francis KL Chan; Joseph JY Sung. / Source: Dissertation Abstracts International, Volume: 72-01, Section: B, page: . / Thesis (M.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 193-235). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web.

We aimed to evaluate the endothelial function by combining RHI measurements and specific biochemical markers in the children with possible risk of premature manifestation of atherosclerosis and in the control group of healthy children. In all, 124 children (of which 106 patients divided into five groups according to diagnosis - type 1 diabetes mellitus, Crohn's disease, cystic fibrosis, familial hypercholesterolemia and acute lymphoblastic leukemia and 18 healthy controls) were enrolled in the study. During the study, we measured RHI using a new plethysmographic method and further evaluated biochemical markers of endothelial dysfunction (ADMA, E-selectin, hsCRP and VCAM) and lipidogram in individual groups of children. The primary objective of our study was the determination of RHI and biochemical parameters in healthy subjects and in selected risk groups of children (type 1 diabetes mellitus, Crohn's disease, cystic fibrosis, familial hypercholesterolemia and children after successful treatment of acute lymphoblastic leukemia). At the same time, we compared patients from individual groups with the control group. We found significantly elevated RHI values in groups of children with type 1 diabetes, Crohn's disease, cystic fibrosis, and children after successful treatment of acute lymphoblastic leukemia....

La presencia de microorganismos patógenos en alimentos es uno de los problemas esenciales en salud pública, y las enfermedades producidas por los mismos es una de las causas más importantes de enfermedad. Por tanto, la aplicación de controles microbiológicos dentro de los programas de aseguramiento de la calidad es una premisa para minimizar el riesgo de infección de los consumidores. Los métodos microbiológicos clásicos requieren, en general, el uso de pre-enriquecimientos no-selectivos,enriquecimientos selectivos, aislamiento en medios selectivos y la confirmación posterior usando pruebas basadas en la morfología, bioquímica y serología propias de cada uno de los microorganismos objeto de estudio. Por lo tanto, estos métodos son laboriosos, requieren un largo proceso para obtener resultados definitivos y, además, no siempre pueden realizarse. Para solucionar estos inconvenientes se han desarrollado diversas metodologías alternativas para la detección identificación y cuantificación de microorganismos patógenos de origen alimentario, entre las que destacan los métodosinmunológicos y moleculares. En esta última categoría, la técnica basada en la reacción en cadena de la polimerasa (PCR) se ha convertido en la técnica diagnóstica más popular en microbiología, y recientemente, la introducción de una mejora de ésta, la PCR a tiempo real, ha producido una segunda revolución en la metodología diagnóstica molecular, como pude observarse por el número creciente de publicaciones científicas y la aparición continua de nuevos kits comerciales. La PCR a tiempo real es unatécnica altamente sensible -detección de hasta una molécula- que permite la cuantificación exacta de secuencias de ADN específicas de microorganismos patógenos de origen alimentario. Además, otras ventajas que favorecen su implantación potencial en laboratorios de análisis de alimentos son su rapidez, sencillez y el formato en tubo cerrado que puede evitar contaminaciones post-PCR y favorece la automatización y un alto rendimiento. En este trabajo se han desarrollado técnicas moleculares (PCR y NASBA) sensibles y fiables para la detección, identificación y cuantificación de bacterias patogénicas de origen alimentario (Listeria spp., Mycobacterium avium subsp. paratuberculosis y Salmonella spp.). En concreto, se han diseñado y optimizado métodos basados en la técnica de PCR a tiempo real para cada uno de estos agentes: L. monocytogenes, L. innocua, Listeria spp. M. avium subsp. paratuberculosis, y también se ha optimizado yevaluado en diferentes centros un método previamente desarrollado para Salmonella spp. Además, se ha diseñado y optimizado un método basado en la técnica NASBA para la detección específica de M. avium subsp. paratuberculosis. También se evaluó la aplicación potencial de la técnica NASBA para la detección específica de formas viables de este microorganismo. Todos los métodos presentaron una especificidad del 100 % con una sensibilidad adecuada para su aplicación potencial a muestras reales de alimentos. Además, se han desarrollado y evaluado procedimientos de preparación de las muestras en productos cárnicos, productos pesqueros, leche y agua. De esta manera se han desarrollado métodos basados en la PCR a tiempo real totalmente específicos y altamente sensibles para la determinación cuantitativa de L. monocytogenes en productoscárnicos y en salmón y productos derivados como el salmón ahumado y de M. avium subsp. paratuberculosis en muestras de agua y leche. Además este último método ha sido también aplicado para evaluar la presencia de este microorganismo en el intestino de pacientes con la enfermedad de Crohn's, a partir de biopsias obtenidas de colonoscopia de voluntarios afectados.En conclusión, este estudio presenta ensayos moleculares selectivos y sensibles para la detección de patógenos en alimentos (Listeria spp., Mycobacterium avium subsp. paratuberculosis) y para una rápida e inambigua identificación de Salmonella spp. La exactitud relativa de los ensayos ha sido excelente, si se comparan con los métodos microbiológicos de referencia y pueden serusados para la cuantificación de tanto ADN genómico como de suspensiones celulares. Por otro lado, la combinación con tratamientos de preamplificación ha resultado ser de gran eficiencia para el análisis de las bacterias objeto de estudio. Por tanto, pueden constituir una estrategia útil para la detección rápida y sensible de patógenos en alimentos y deberían ser una herramienta adicional al rango de herramientas diagnósticas disponibles para el estudio de patógenos de origen alimentario. / The presence of pathogens in foods is among the most serious public health concerns, and the diseases produced by them are a major cause of morbidity. Consequently, the application of microbiological control within the quality assessment programs in the food industry is a premise to minimize the risk of infection for the consumer. Classical microbiological methods involve, in general, the use of a non-selective pre-enrichment, selective enrichment, isolation on selective media, and subsequent confirmation using morphological, biochemical and/or serological tests. Thus, they are laborious, time consuming and not always reliable (e.g. in viable but non-culturable VBNC forms). A number of alternative, rapid and sensitive methods for the detection, identification and quantification of foodborne pathogens have been developed to overcome these drawbacks. PCR has become the most popular microbiological diagnostic method, and recently, the introduction of a development of this technique, RTi-PCR, has produced a second revolution in the molecular diagnostic methodology in microbiology. RTi-PCR is highly sensitive and specific. Moreover, it allows accurate quantification of the bacterial target DNA. Main advantages of RTi-PCR for its application in diagnostic laboratories include quickness, simplicity, the closed-tube format that avoids risks of carryover contaminations and the possibility of high throughput and automation.In this work, specific, sensitive and reliable analytical methods based on molecular techniques (PCR and NASBA) were developed for the detection, identification and quantification of foodborne pathogens (Listeria spp., Mycobacterium avium subsp. paratuberculosis and Salmonella spp.). Real-time PCR based methods were designed and optimised for each one of these target bacteria: L. monocytogenes, L. innocua, Listeria spp. M. avium subsp. paratuberculosis, and also a real-time PCR basedmethod previously described for Salmonella spp. was optimised and multicenter evaluated. In addition, an NASBA-based method was designed and optimised for the specific detection of M. avium subsp. paratuberculosis. The potential application of the NASBA technique for specific detection of viable M. avium subsp. paratuberculosis cells was also evaluated.All the amplification-based methods were 100 % specific and the sensitivity achieved proved to be fully suitable for further application in real food samples. Furthermore, specific pre-amplification procedures were developed and evaluated on meatproducts, seafood products, milk and water samples. Thus, fully specific and highly sensitive real-time PCR-based methods were developed for quantitative detection of L. monocytogenes on meat and meat products and on salmon and cold smoked salmon products; and for quantitative detection of M. avium subsp. paratuberculosis on water and milk samples. The M. avium subsp. paratuberculosis-specific real-time PCR-based method was also applied to evaluate the presence of this bacterium in the bowelof Crohn's disease patients using colonic biopsy specimens form affected and unaffected volunteers. In addition, fully specific and highly sensitive real-time NASBA-based methods were developed for detection of M. avium subsp. paratuberculosis on water and milk samples.In conclusion, this study reports selective and sensitive amplification-based assays for the quantitative detection of foodborne pathogens (Listeria spp., Mycobacterium avium subsp. paratuberculosis and) and for a quick and unambiguously identification of Salmonella spp. The assays had an excellent relative accuracy compared to microbiological reference methods and can be used for quantification of genomic DNA and also cell suspensions. Besides, in combination with sample pre-amplification treatments,they work with high efficiency for the quantitative analysis of the target bacteria. Thus, they could be a useful strategy for a quick and sensitive detection of foodborne pathogens in food products and which should be a useful addition to the range of diagnostic tools available for the study of these pathogens.