Chronic acid reflux causes cellular damage and inflammation in the lower esophagus. Due to these irritating insults, the squamous epithelium is replaced by metaplastic epithelium, which is a risk factor for the development of esophageal adenocarcinoma (EAC). In this study, we investigated the acid susceptibility in a Barrett’s cell culture in vitro model, using six cell lines, derived from squamous epithelium (EPC1 and EPC2), metaplasia (CP-A), dysplasia (CP-B), and EAC (OE33 and OE19) cells. Cells exposed to acidic pH showed a decreased viability dependent on time, pH, and progression status in the Barrett’s sequence, with the highest acid susceptibility in the squamous epithelium (EPC1 and EPC2), and the lowest in EAC cells. Acid pulsing was accompanied with an activation of the Nrf2/Keap1- and the NFκB-pathway, resulting in an increased expression of HO1—independent of the cellular context. OE33 showed a decreased responsiveness towards 5-FU, when the cells were grown in acidic conditions (pH 6 and pH 5.5). Our findings suggest a strong damage of squamous epithelium by gastroesophageal reflux, while Barrett’s dysplasia and EAC cells apparently exert acid-protective features, which lead to a cellular resistance against acid reflux.

INTRODUÇÃO: No mundo ocidental, a prevalência de adenocarcinoma da junção esofagogástrica vem crescendo nas últimas décadas. Atualmente, é aceito que o adenocarcinoma do esôfago se desenvolve de uma lesão pré-maligna: esôfago de Barrett. Este carcinoma é de difícil diagnóstico nos seus estágios iniciais, o que resulta em uma mortalidade significativa. O estudo da biologia molecular tem demonstrado que grande parte dos tumores malignos tem origem na interação entre o componente hereditário e influências externas, que em indivíduos predispostos podem ocasionar alterações genéticas que influenciem o controle da diferenciação e crescimento celular. O p21 (WAF1/CIP1) tem um papel fundamental na regulação do ciclo celular, e sua expressão imunoistoquímica tem sido estudada em diversos tumores, mostrando influência no prognóstico de várias neoplasias. OBJETIVO: Verificar a prevalência da expressão da proteína p21 em pacientes com adenocarcinoma de esôfago diagnosticados nos últimos cinco anos no Grupo de Cirurgia de Esôfago e Estômago do Hospital de Clínicas de Porto Alegre (GCEE/HCPA). METODOLOGIA: A população em estudo foi constituída de 42 pacientes com adenocarcinoma de esôfago diagnosticados no GCEE/HCPA entre janeiro de 1998 e dezembro de 2002. A expressão da proteína p21 foi realizada por meio de imunoistoquímica, com anticorpo primário, p21, clone SX118, código M7202 da DAKO, e avaliada de acordo com o Sistema de Escore de Imunorreatividade (Immunoreactive scoring system – IRS). RESULTADOS: Foram estudados 42 pacientes. 83,3% eram do sexo masculino, com idade superior a 40 anos. Destes, 56,2% foram submetidos a procedimentos cirúrgicos com intenção curativa: Gastrectomia total e Esofagogastrectomia transiatal. Os demais foram submetidos à cirurgia paliativa ou não sofreram tratamento cirúrgico. Apenas cinco pacientes receberam tratamento adjuvante com quimioterapia e radioterapia, isoladas ou combinadas. Quanto ao estadiamento, 78,6% dos pacientes apresentavam doença avançada, estádios III e IV. Apenas 9 apresentaram positividade para o p21, quando considerado o Sistema de Escore de Imunorreatividade (em que p21+ é ³ 3). CONCLUSÃO: A proteína p21 esteve expressa em 9 dos 42 pacientes (21,4%) com adenocarcinoma de esôfago diagnosticados nos últimos cinco anos no Grupo de Cirurgia de Esôfago e Estômago do Hospital de Clínicas de Porto Alegre. Nessa casuística, o acúmulo de p21 não se mostrou essencial no processo de carcinogênese do adenocarcinoma esofágico. / INTRODUCTION: In western societies, the prevalence of adenocarcinoma of the gastroesophageal junction has increased in recent years. It is commonly accepted today that esophageal adenocarcinoma develops from a premalignant lesion: Barrett’s esophagus. This type of carcinoma is hardly diagnosed at early stages, which results in significant mortality. Molecular biology studies have shown that most malignant tumors originate from the interaction between inherited characteristics and external factors, which may cause genetic changes that interfere with the control over the differentiation and growth of cells in susceptible individuals. p21 (WAF1/CIP1) has a key role in the regulation of the cell cycle, and its immunohistochemical expression has been investigated in several tumors, showing that it influences the prognosis of various neoplasms. OBJECTIVE: To check the prevalence of p21 protein expression in patients with esophageal adenocarcinoma diagnosed in the last five years by the Group for Surgeries of the Esophagus and Stomach of Hospital de Clínicas de Porto Alegre (GCEE/HCPA). METHODS: The study population consisted of 42 patients with esophageal adenocarcinoma diagnosed by the GCEE/HCPA between January 1998 and December 2002. The expression of p21 protein was determined by immunohistochemistry using primary antibody, p21, clone SX118, code M7202 (Dako), and assessed according to the Immunoreactive scoring system (IRS). RESULTS: Of 42 analyzed patients, 83.3% were male and older than 40 years. Among these, 56.2% were submitted to curative resection: total gastrectomy and transhiatal esophagogastrectomy. The remaining patients were submitted to palliative surgery or did not undergo any surgical treatment. Only five patients received adjuvant chemotherapy and radiation therapy, either alone or combined. Advanced disease (stages III and IV) was detected in 78.6% of the patients. Only nine patients were positive for p21, according to the immunoreactive scoring system (p21+ ³ 3). CONCLUSION: p21 was expressed in 9 of 42 patients (21.4%) with esophageal adenocarcinoma diagnosed in the last five years by the Group for Surgeries of the Esophagus and Stomach of Hospital de Clínicas de Porto Alegre. In our patient population, the accumulation of p21 did not play a key role in the carcinogenesis of esophageal adenocarcinoma.

INTRODUÇÃO: No mundo ocidental, a prevalência de adenocarcinoma da junção esofagogástrica vem crescendo nas últimas décadas. Atualmente, é aceito que o adenocarcinoma do esôfago se desenvolve de uma lesão pré-maligna: esôfago de Barrett. Este carcinoma é de difícil diagnóstico nos seus estágios iniciais, o que resulta em uma mortalidade significativa. O estudo da biologia molecular tem demonstrado que grande parte dos tumores malignos tem origem na interação entre o componente hereditário e influências externas, que em indivíduos predispostos podem ocasionar alterações genéticas que influenciem o controle da diferenciação e crescimento celular. O p21 (WAF1/CIP1) tem um papel fundamental na regulação do ciclo celular, e sua expressão imunoistoquímica tem sido estudada em diversos tumores, mostrando influência no prognóstico de várias neoplasias. OBJETIVO: Verificar a prevalência da expressão da proteína p21 em pacientes com adenocarcinoma de esôfago diagnosticados nos últimos cinco anos no Grupo de Cirurgia de Esôfago e Estômago do Hospital de Clínicas de Porto Alegre (GCEE/HCPA). METODOLOGIA: A população em estudo foi constituída de 42 pacientes com adenocarcinoma de esôfago diagnosticados no GCEE/HCPA entre janeiro de 1998 e dezembro de 2002. A expressão da proteína p21 foi realizada por meio de imunoistoquímica, com anticorpo primário, p21, clone SX118, código M7202 da DAKO, e avaliada de acordo com o Sistema de Escore de Imunorreatividade (Immunoreactive scoring system – IRS). RESULTADOS: Foram estudados 42 pacientes. 83,3% eram do sexo masculino, com idade superior a 40 anos. Destes, 56,2% foram submetidos a procedimentos cirúrgicos com intenção curativa: Gastrectomia total e Esofagogastrectomia transiatal. Os demais foram submetidos à cirurgia paliativa ou não sofreram tratamento cirúrgico. Apenas cinco pacientes receberam tratamento adjuvante com quimioterapia e radioterapia, isoladas ou combinadas. Quanto ao estadiamento, 78,6% dos pacientes apresentavam doença avançada, estádios III e IV. Apenas 9 apresentaram positividade para o p21, quando considerado o Sistema de Escore de Imunorreatividade (em que p21+ é ³ 3). CONCLUSÃO: A proteína p21 esteve expressa em 9 dos 42 pacientes (21,4%) com adenocarcinoma de esôfago diagnosticados nos últimos cinco anos no Grupo de Cirurgia de Esôfago e Estômago do Hospital de Clínicas de Porto Alegre. Nessa casuística, o acúmulo de p21 não se mostrou essencial no processo de carcinogênese do adenocarcinoma esofágico. / INTRODUCTION: In western societies, the prevalence of adenocarcinoma of the gastroesophageal junction has increased in recent years. It is commonly accepted today that esophageal adenocarcinoma develops from a premalignant lesion: Barrett’s esophagus. This type of carcinoma is hardly diagnosed at early stages, which results in significant mortality. Molecular biology studies have shown that most malignant tumors originate from the interaction between inherited characteristics and external factors, which may cause genetic changes that interfere with the control over the differentiation and growth of cells in susceptible individuals. p21 (WAF1/CIP1) has a key role in the regulation of the cell cycle, and its immunohistochemical expression has been investigated in several tumors, showing that it influences the prognosis of various neoplasms. OBJECTIVE: To check the prevalence of p21 protein expression in patients with esophageal adenocarcinoma diagnosed in the last five years by the Group for Surgeries of the Esophagus and Stomach of Hospital de Clínicas de Porto Alegre (GCEE/HCPA). METHODS: The study population consisted of 42 patients with esophageal adenocarcinoma diagnosed by the GCEE/HCPA between January 1998 and December 2002. The expression of p21 protein was determined by immunohistochemistry using primary antibody, p21, clone SX118, code M7202 (Dako), and assessed according to the Immunoreactive scoring system (IRS). RESULTS: Of 42 analyzed patients, 83.3% were male and older than 40 years. Among these, 56.2% were submitted to curative resection: total gastrectomy and transhiatal esophagogastrectomy. The remaining patients were submitted to palliative surgery or did not undergo any surgical treatment. Only five patients received adjuvant chemotherapy and radiation therapy, either alone or combined. Advanced disease (stages III and IV) was detected in 78.6% of the patients. Only nine patients were positive for p21, according to the immunoreactive scoring system (p21+ ³ 3). CONCLUSION: p21 was expressed in 9 of 42 patients (21.4%) with esophageal adenocarcinoma diagnosed in the last five years by the Group for Surgeries of the Esophagus and Stomach of Hospital de Clínicas de Porto Alegre. In our patient population, the accumulation of p21 did not play a key role in the carcinogenesis of esophageal adenocarcinoma.

INTRODUÇÃO: No mundo ocidental, a prevalência de adenocarcinoma da junção esofagogástrica vem crescendo nas últimas décadas. Atualmente, é aceito que o adenocarcinoma do esôfago se desenvolve de uma lesão pré-maligna: esôfago de Barrett. Este carcinoma é de difícil diagnóstico nos seus estágios iniciais, o que resulta em uma mortalidade significativa. O estudo da biologia molecular tem demonstrado que grande parte dos tumores malignos tem origem na interação entre o componente hereditário e influências externas, que em indivíduos predispostos podem ocasionar alterações genéticas que influenciem o controle da diferenciação e crescimento celular. O p21 (WAF1/CIP1) tem um papel fundamental na regulação do ciclo celular, e sua expressão imunoistoquímica tem sido estudada em diversos tumores, mostrando influência no prognóstico de várias neoplasias. OBJETIVO: Verificar a prevalência da expressão da proteína p21 em pacientes com adenocarcinoma de esôfago diagnosticados nos últimos cinco anos no Grupo de Cirurgia de Esôfago e Estômago do Hospital de Clínicas de Porto Alegre (GCEE/HCPA). METODOLOGIA: A população em estudo foi constituída de 42 pacientes com adenocarcinoma de esôfago diagnosticados no GCEE/HCPA entre janeiro de 1998 e dezembro de 2002. A expressão da proteína p21 foi realizada por meio de imunoistoquímica, com anticorpo primário, p21, clone SX118, código M7202 da DAKO, e avaliada de acordo com o Sistema de Escore de Imunorreatividade (Immunoreactive scoring system – IRS). RESULTADOS: Foram estudados 42 pacientes. 83,3% eram do sexo masculino, com idade superior a 40 anos. Destes, 56,2% foram submetidos a procedimentos cirúrgicos com intenção curativa: Gastrectomia total e Esofagogastrectomia transiatal. Os demais foram submetidos à cirurgia paliativa ou não sofreram tratamento cirúrgico. Apenas cinco pacientes receberam tratamento adjuvante com quimioterapia e radioterapia, isoladas ou combinadas. Quanto ao estadiamento, 78,6% dos pacientes apresentavam doença avançada, estádios III e IV. Apenas 9 apresentaram positividade para o p21, quando considerado o Sistema de Escore de Imunorreatividade (em que p21+ é ³ 3). CONCLUSÃO: A proteína p21 esteve expressa em 9 dos 42 pacientes (21,4%) com adenocarcinoma de esôfago diagnosticados nos últimos cinco anos no Grupo de Cirurgia de Esôfago e Estômago do Hospital de Clínicas de Porto Alegre. Nessa casuística, o acúmulo de p21 não se mostrou essencial no processo de carcinogênese do adenocarcinoma esofágico. / INTRODUCTION: In western societies, the prevalence of adenocarcinoma of the gastroesophageal junction has increased in recent years. It is commonly accepted today that esophageal adenocarcinoma develops from a premalignant lesion: Barrett’s esophagus. This type of carcinoma is hardly diagnosed at early stages, which results in significant mortality. Molecular biology studies have shown that most malignant tumors originate from the interaction between inherited characteristics and external factors, which may cause genetic changes that interfere with the control over the differentiation and growth of cells in susceptible individuals. p21 (WAF1/CIP1) has a key role in the regulation of the cell cycle, and its immunohistochemical expression has been investigated in several tumors, showing that it influences the prognosis of various neoplasms. OBJECTIVE: To check the prevalence of p21 protein expression in patients with esophageal adenocarcinoma diagnosed in the last five years by the Group for Surgeries of the Esophagus and Stomach of Hospital de Clínicas de Porto Alegre (GCEE/HCPA). METHODS: The study population consisted of 42 patients with esophageal adenocarcinoma diagnosed by the GCEE/HCPA between January 1998 and December 2002. The expression of p21 protein was determined by immunohistochemistry using primary antibody, p21, clone SX118, code M7202 (Dako), and assessed according to the Immunoreactive scoring system (IRS). RESULTS: Of 42 analyzed patients, 83.3% were male and older than 40 years. Among these, 56.2% were submitted to curative resection: total gastrectomy and transhiatal esophagogastrectomy. The remaining patients were submitted to palliative surgery or did not undergo any surgical treatment. Only five patients received adjuvant chemotherapy and radiation therapy, either alone or combined. Advanced disease (stages III and IV) was detected in 78.6% of the patients. Only nine patients were positive for p21, according to the immunoreactive scoring system (p21+ ³ 3). CONCLUSION: p21 was expressed in 9 of 42 patients (21.4%) with esophageal adenocarcinoma diagnosed in the last five years by the Group for Surgeries of the Esophagus and Stomach of Hospital de Clínicas de Porto Alegre. In our patient population, the accumulation of p21 did not play a key role in the carcinogenesis of esophageal adenocarcinoma.

Abstract Incidence of esophageal adenocarcinoma is rising rapidly in Western countries. The main risk factor for esophageal adenocarcinoma is Barrett’s esophagus. Barrett’s esophagus results from long-term gastroesophageal reflux disease. The gastrointestinal tract is colonized by bacteria, fungi and viruses forming the alimentary tract microbiome. Microbiome transformation is involved in pathogenesis of alimentary tract cancer and also in the development of Barrett’s metaplasia. Toll-like receptors (TLR) are molecules of the innate immune system and they are involved in bacterial and viral recognition and regulation of immune functions in the host and cancer cells. This thesis examined the effect of alimentary tract microbiome and cancer- on the function of TLRs in normal gastrointestinal epithelial cells. An additional focus of the thesis was also to assess the carcinogenetic effect of TLRs 1–9 in Barrett’s esophagus metaplasia – dysplasia – carcinoma sequence. Study material consisted of: a patient cohort, organ donors, conventional and germ-free mice. TLRs are expressed also in a “microbe-free” gut. There were significant differences in all TLRs between small- and large intestine of conventional mice and in humans. In germ-free mice that difference was not observed. Normal tissue sampled adjacent to the tumors of cancer patients can be used as controls in immunohistochemical TLR studies in gastrointestinal cancer Clinical data indicate that TLRs linearly increase toward dysplasia in Barrett’s esophagus. High cytoplasmic and nuclear TLR4 expression and TLR1 and 8 nuclear immunoreactivity in esophageal adenocarcinoma are associated with metastatic disease and poor prognosis. Based on our results, bacteria seem to downregulate TLR expression of the intestine. TLRs 1–9 apparently have a role in malignant progression of Barrett’s dysplasia. TLR1, TLR4 and TLR8 may represent a novel therapeutic target in esophageal adenocarcinoma. / Tiivistelmä Ruokatorven adenokarsinooma on länsimaissa nopeasti yleistyvä syöpätyyppi. Tämän syöpätyypin tärkein riskitekijä on Barrettin ruokatorvi, joka kehittyy pitkään jatkuneen gastroesofageaalisen refluksitaudin pohjalta. Ruuansulatuskanavassa on suuri määrä bakteereja, sieniä ja viruksia, jotka muodostavat yhdessä ruuansulatuskanavan mikrobiomin. Normaalin mikrobiomin muutokset ovat yhteydessä usean eri ruuansulatuskanavan syövän patogeneesiin ja myös Barrettin ruokatorven muodostumiseen. Tollin kaltaiset reseptorit ovat luontaisen immuniteetin molekyylejä, jotka osallistuvat bakteerien ja virusten tunnistukseen ja sääntelevät immuunivastetta sekä normaalitilanteessa että syövissä. Väitöskirjassa tutkitaan ruuansulatuskanavan mikrobiomin ja syövän vaikutuksia normaalien epiteelisolujen TLR:ien toimintaan. Lisäksi selvitetään TLR:ien karsinogeneettisiä vaikutuksia Barrettin ruokatorven metaplasia- dysplasia -adenokarsinoomasekvenssissä. Tutkimusmateriaalina käytetään potilaskohortista ja elinluovutuksista peräisin olevia potilasnäytteitä sekä normaalien ja bakteerittomien hiirien näytteitä. Tuloksemme osoittavat, että TLR:t ilmentyvät myös bakteerittomassa ruuansulatuskanavassa, ja TLR:en ilmentyminen oli merkittävästi voimakkaampaa ohutsuolessa kuin paksusuolessa normaaleilla hiirillä ja ihmisillä. Tätä eroa ei havaittu bakteerittomilla hiirillä. Ruuansulatuskanavan syöpien viereistä ja sen altistamaa tervettä kudosta voidaan käyttää terveenä kontrollina immunohistokemiallisissa TLR- tutkimuksissa. Kliinisessä aineistossa TLR:ien ilmentyminen kasvaa lineaarisesti kohti dysplasiaa Barrettin ruokatorvessa. TLR4:n korkea ilmentyminen solulimassa ja tumassa sekä TLR8:n ilmentyminen tumassa ovat yhteydessä metastaattiseen tautiin ja huonoon ennusteeseen. Tulosten perusteella bakteerit näyttävät heikentävän TLR:ien toimintaa suolistossa. Lisäksi kaikilla tutkituilla TLR:illä (1–9) näyttää olevan osuutta Barrettin dysplasian etenemisessä kohti syöpää. TLR1, TLR4 ja TLR8 ovat mahdollisia terapeuttisia kohteita ruokatorven adenokarsinoomassa.

L'œsophage et la trachée proviennent du diverticule endodermique du tube de l'intestin antérieur au cours de l'embryogenèse. Des événements cellulaires et moléculaires bien régulés et organisés entraînent la séparation du tube de l'intestin antérieur en œsophage et trachée. Cette séparation est encore mal connue et la perturbation de ce processus se traduit par une anomalie congénitale sévère telle qu'une l’atrésie de l'œsophage avec ou sans fistule trachéo-œsophagienne (AO/FTO). L'AO/FTO est l'une des malformations congénitales gastro-intestinales les plus courantes affectant 1 naissance sur 3000. Cette malformation nécessite une intervention chirurgicale urgente à la naissance et est fréquemment associée à une morbidité à long terme. Les mécanismes sous-jacents au développement embryonnaire de l'AO/FTO sont mal compris. Les modèles animaux ont été largement utilisés pour comprendre les maladies humaines depuis des décennies et ont considérablement contribué à la compréhension du développement de l'œsophage. Cependant, des différences structurelles et morphologiques clés existent entre l'œsophage humain et animal, ce qui nécessite un modèle plus fiable pour comprendre le développement trachée-œsophagien. Les cellules souches pluripotentes induites par l'homme ont été un outil précieux pour comprendre l'organogenèse en imitant le développement et en déchiffrant les mécanismes qui conduisent à des maladies congénitales et acquises. Cette thèse se concentre donc sur l'utilisation de cellules souches pluripotentes induites (IPS) par des patients pour déchiffrer les mécanismes de signalisation impliqués dans le développement de l'œsophage et les maladies congénitales telles que l’OA/FTO. Il étudie également l'une des maladies œsophagiennes acquises possibles, comme l'œsophage de Barrett. Nous avons orienté la différenciation des IPS saines et dérivées de patients vers différents stades de développement, tels que l'endoderme définitif, l'intestin antérieur, l'épithélium œsophagien et trachéal. De plus, l'épithélium œsophagien a été développé davantage dans un environnement tridimensionnel sans matrice pour générer des organoïdes œsophagiens matures. À chaque étape de la progression du développement, des analyses d'immunofluorescence, de qPCR et de séquençage d'ARN ont été effectuées. Nos résultats suggèrent que l'expression des marqueurs endodermiques CXCR4, SOX17, et GATA4 était similaire dans les cellules différenciées des patients et des cellules saines. Cependant, au stade de l'intestin antérieur, nous avons observé une diminution significative de l'expression des gènes et des protéines du facteur transcriptionnel clé SOX2 dans les cellules dérivées du patient. De plus, en utilisant le séquençage d'ARN à molécule unique, nous avons observé que les gènes critiques GSTM1, et RAB37 impliqués dans la morphogenèse cellulaire et associés à l’OA/FTO étaient dérégulés au stade de l'intestin antérieur dans les cellules dérivées du patient. Nous avons également observé une augmentation significative de l'expression du facteur de transcription NKX2.1 habituellement exprimé uniquement dans les cellules trachéales, dans l'épithélium oesophagien dérivé du patient. NKX2.1 est maintenue dans les organoïdes oesophagiens matures même après 2 mois. Ensuite, nous voulions valider l'utilisation potentielle de nos organoïdes dérivés des IPS pour modéliser les maladies acquises de l'œsophage telles que l'œsophage de Barrett. Nous avons induit une métaplasie ou transformation épithéliale avec surexpression de BMP4 dans des organoïdes de l'œsophage sains et dérivés du patient sur une période d'un mois. Nos résultats préliminaires montrent que les organoïdes de l'œsophage dérivés des patients exprimaient des niveaux d'ARNm plus élevés de MUC5AC, un marqueur épithélial cylindrique par rapport au groupe sain. Cela suggère une plus grande sensibilité de l'organoïde de l'œsophage dérivé du patient aux changements epitheliales métaplasiques. En conclusion, nous avons développé les premiers organoïdes œsophagiens tridimensionnels matures sans matrice différenciés des patients OA/FTO et identifié une signature moléculaire unique dans les cellules dérivées du patient au cours de la différenciation dirigée de l'œsophage. De plus, sur la base des résultats préliminaires, nous avons pu confirmer l'incidence plus élevée de l'œsophage de Barrett chez les patients OA/FTO par rapport au groupe sain. Notre travail met donc en évidence l'importance de l'utilisation des IPS dérivées des patients pour modéliser les maladies œsophagiennes congénitales et acquises afin de fournir de nouvelles informations sur le développement des organes au cours de l'embryogenèse. / The esophagus and trachea originate from the endodermal diverticulum of the anterior foregut tube during embryogenesis. Well-regulated and organized cellular and molecular events result in the compartmentalization of the anterior foregut tube into the esophagus and trachea. This compartmentalization is still poorly understood and disruption in this process results in a severe congenital anomaly such as esophageal atresia with or without tracheoesophageal fistula (EA/TEF). EA/TEF is one of the most common gastrointestinal congenital defects affecting 1 in 3,000 births. This malformation requires urgent surgery at birth and is frequently associated with long-term morbidity. The mechanisms underlying the embryonic development of EA/TEF are poorly understood. Animal models have been widely used to understand human diseases for decades and have significantly contributed to the understanding of esophageal development. However, key structural and morphological differences exist between human and animal esophagus, thus necessitating a more reliable model to understand trachea-esophageal development. Human induced pluripotent stem cells (iPSC) have been a valuable tool to understand organogenesis by mimicking development and deciphering mechanisms that lead to congenital and acquired diseases. This thesis therefore focuses on the use of patient-derived induced pluripotent stem cells to decipher signaling mechanisms involved in esophageal development and congenital diseases such as EA/TEF. It also focuses on one of the possible acquired esophageal diseases, namely, Barrett’s esophagus. We directed the differentiation of healthy and patient-derived iPSCs toward different developmental stages, such as definitive endoderm, anterior foregut, esophageal and tracheal epithelium. Furthermore, the esophageal epithelium was matured further in a matrix free 3-dimensional environment to generate mature esophageal organoids. At each stage of development progression, immunofluorescence, qPCR, and RNA sequencing analysis were performed. Our findings suggest that the expression of endodermal markers CXCR4, SOX17, and GATA4, were similar in both patient and healthy differentiated cells. However, at the anterior foregut stage, we observed a significant decrease in the gene and protein expression of key transcription factor SOX2 in patient-derived cells. Furthermore, using nanopore RNA sequencing, we observed that critical genes GSTM1, and RAB7 involved in cellular morphogenesis and associated with EA/TEF to be dysregulated at the anterior foregut stage in patient-derived cells. We also observed a significant increase in the expression of transcription factor NKX2.1, usually expressed only in tracheal cells, in the patient-derived esophageal epithelium. NKX2.1 expression was maintained in matured esophageal organoids even after 2 months. Next, we wanted to validate the potential use of our PSC-derived organoids to model acquired esophagus diseases such as Barrett’s esophagus (BE). We induced epithelial metaplasia with BMP4 overexpression in healthy and patient-derived esophagus organoids over a 1-month period. Our preliminary results show that patient-derived esophagus organoids expressed higher mRNA levels of MUC5AC, an epithelial columnar marker compared with the healthy group. This suggests a higher susceptibility of patient-derived esophagus organoid to metaplastic changes. In conclusion, we developed the first matrix free mature 3-dimensional esophageal organoids differentiated from EA/TEF patient-derived and identified a unique molecular signature in patient derived cells during directed esophagus differentiation. Furthermore, based on the preliminary results, we could confirm the higher incidence of Barrett’s esophagus in EA/TEF patients compared with the healthy group. Our work therefore highlights the significance of using patient-derived iPSCs to model congenital and acquired esophageal diseases to yield new insights on organ development during embryogenesis. It lays the foundation for a personalized medical approach to other diseases and the ones affecting the whole gastrointestinal system in both children and adults.