Addressing tumor heterogeneity in esophageal adenocarcinoma through different molecular approaches

Several studies have shown epidemiologic, clinical, immune-histochemical and molecular differences among esophageal adenocarcinomas (EAC). Since pathogenesis and biology of this tumor are far to be well defined, our study aimed to examine intra- and inter-tumor heterogeneity and to solve crucial controversies through different molecular approaches. Target sequencing was performed for sorted cancer subpopulations from formalin embedded material obtained from 38 EACs, not treated with neoadjuvant therapy. 35 out 38 cases carried at least one somatic mutation, not present in the corresponding sorted stromal cells. 73.7% of cases carried mutations in TP53 and 10.5% in CDKN2A. Mutations in other genes occurred at lower frequency, including HNF1A, not previously associated with EAC. Sorting allowed us to isolate clones with different mutational loads and/or additional copy number amplifications, confirming the high intra-tumor heterogeneity of these cancers. In our cohort TP53 gene abnormalities correlated with a better survival (P = 0.028); conversely, loss of SMAD4 protein expression was associated with a higher recurrence rate (P = 0.015). Shifting the focus on the epigenetic characterization of EAC, miR-221 and miR-483-3p resulted upregulated from the MicroRNA Array card analysis and confirmed with further testing. The up-regulation of both miRNAs correlated with clinical outcomes, in particular with a reduced cancer-specific survival (miR483-3p P=0.0293; miR221 P=0.0059). In vitro analyses demonstrated an increase for miR-483-3p (fold-change=2.7) that appear to be inversely correlated with SMAD4 expression in FLO-1 cell-line. In conclusion, selective sorting allowed to define the real mutation status and to isolate different cancer subclones. MiRNA expression analysis revealed a significant up-regulation of miR-221 and miR-483-3p, which correlated with worst prognosis, implying that they can be considered oncogenic factors in EAC. Therefore, cell sorting technologies, coupled with next generation sequencing, and the analysis of microRNA profiles seem to be promising strategies to guide treatment and help classify cancer prognosis.

Tumor heterogeneity in Esophageal Adenocarcinoma: a genomic approach

INTRODUCTION: Esophageal adenocarcinoma (EAC) is a severe malignancy in terms of prognosis and mortality rate. Because its great genetic heterogeneity, disputes regarding classification, prevention and treatments are still unsolved. AIM: We investigated intra- and inter-EAC heterogeneity by defining EAC’s somatic mutational profile and the role of candidate microRNAs, to correlate the molecular profile of tumors to clinical outcomes and to identify biomarkers for classification. METHODS: 38 EAC cases were analyzed via high-throughput cell sorting technology combined with targeted sequencing and whole genome low-pass sequencing. Targeted sequencing of further 169 cases was performed to widen the study. miR221 and miR483-3p expression was profiled via qPCR in 112 EACs and correlation with clinical outcomes was investigated. RESULTS: 35/38 EACs carried at least one somatic mutation absent in stromal cells. TP53 was found mutated in 73.7% of cases. Selective sorting revealed tumor subclones with different mutational loads and copy number alterations, confirming the high intra-tumor heterogeneity of EAC. Mutations were in most cases at homozygous state, and we identified alterations that were missed with the whole-tumor analysis. Mutations in HNF1A gene, not previously associated with EAC, were identified in both cohorts. Higher expression of miR483-3p and miR221 was associated with poorer cancer specific survival (P=0.0293 and P=0.0059), and recurrence in the Lauren intestinal subtype (P=0.0459 and P=0.0002). Median expression levels of miRNAs were higher in patients with advanced tumor stages. The loss of SMAD4 immunoreactivity was significantly associated with poorer cancer specific survival and recurrence (P=0.0452; P=0.022 respectively). CONCLUSION: Combining selective sorting technology and next generation sequencing allowed to better define EAC inter- and intra-tumor heterogeneity. We identified HNF1A as a new mutated gene associated to EAC that could be involved in tumor progression and promising biomarkers such as SMAD4, miR221 and miR483-3p to identify patients at higher risk for more aggressive tumors.

Identification of molecular biomarkers in esophageal adenocarcinoma

Esophageal adenocarcinoma (EAC) is a severe cancer that has been on the rise in Western nations over the past few decades. It has a high mortality rate and the 5-year survival rate is only 35%–45%. EAC has been included in a group of tumors with one of the highest rates of copy number alterations (CNAs), somatic structural rearrangements, high mutation frequency, with different mutational signatures, and with epigenetic mechanisms. The vast heterogeneity of EAC mutations makes it challenging to comprehend the biology that underlies tumor onset and development, identify prognostic biomarkers, and define a molecular classification to stratify patients. The only way to resolve the current disagreements is through an exhaustive molecular analysis of EAC. We examined the genetic profile of 164 patients' esophageal adenocarcinoma samples (without chemo-radiotherapy). The included patients did not receive neoadjuvant therapies, which can change the genetic and molecular composition of the tumor. Using next-generation sequencing technologies (NGS) at high coverage, we examined a custom panel of 26 cancer-related genes. Over the entire cohort, 337 variants were found, with the TP53 gene showing the most frequent alteration (67.27%). Poorer cancer-specific survival was associated with missense mutations in the TP53 gene (Log Rank P=0.0197). We discovered HNF1alpha gene disruptive mutations in 7 cases that were also affected by other gene changes. We started to investigate its role in EAC cell lines by silencing HNF1alpha to mimic our EAC cohort and we use Seahorse technique to analyze its role in the metabolism in esophageal cell. No significant changes were found in transfected cell lines. We conclude by finding that a particular class of TP53 mutations (missense changes) adversely impacted cancer-specific survival in EAC. HNF1alpha, a new EAC-mutated gene, was found, but more research is required to fully understand its function as a tumor suppressor gene.

Clinicopathological and molecular characterization of gastroesophageal junction (GEJ) adenocarcinoma before age of 40 years

Gastroesophageal junction (GEJ) adenocarcinoma are uncommon before age of 40 years. While certain clinical, pathological and molecular features of GEJ adenocarcinoma in older patients have been extensively studied, these characteristics in the younger population remain to be determined. In the recent literature, a high sensitivity and specificity for the detection of dysplasia and esophageal adenocarcinoma was demonstrated by using multicolor fluorescence in situ hybridization (FISH) DNA probe set specific for the locus specific regions 9p21 (p16), 20q13.2 and Y chromosome. We evaluated 663 patients with GEJ adenocarcinoma and further divided them into 2 age-groups of or= 50 years, rispectively. FISH with selected DNA probe for Y chromosome, locus 9p21 (p16), and locus 20q13.2 was investigated with formalin fixed and parassin embedded tissue from surgical resections of 17 younger and 11 older patients. Signals were counted in > 100 cells with each given histopathological category. The chromosomal aberrations were then compared in the 2 age-groups with the focus on uninvolved squamous and columnar epithelium, intestinal metaplasia (Barrett's mucosa), glandular dysplasia, and adenocarcinoma. Comparisons were performed by the X2 test, Fisher's exact test, Student's t-test and Mann-Whitney U-test as appropriate. Survival was estimated by the Kaplan-Meier method with univariate analysis by the log-rank. Significance was taken at the 5% level. There was no difference in the surgical technique applied in both age groups and most patients underwent Ivor Lewis esophagectomy. Among clinical variables there was a higher incidence of smocking history in older patient group. We identified a progressive loss of Y chromosome from benign squamos epithelium to Barrett's mucosa and glandular dysplasia, and, ultimately, to a near complete loss in adenocarcinoma in both age groups. The young group revealed significantly more losses of 9p21 in both benign and neoplastic cells when compared to the older patients group. In addition, we demonstrated an increase in the percentage of cells showing gain of locus 20q13.2 with progression from benign epithelium through dysplasia to adenocarcinoma with almost the same trend in both the young and the older patients. When compared with the older age-group, younger patients with GEJ adenocarcinoma possess similar known demographics, environmental factors, clinical, and pathologic characteristics. The most commonly detected genetic aberrations of progressive Y chromosomal loss, 9p21 locus loss, and 20q13 gains were similar in the younger and older patients. However the rate of loss of 9p21 is significantly higher in young patients, in both the benign and the neoplastic cells. The loss of 9p21, and possibly, the subsequent inactivation of p16 gene may be one of the molecular mechanisms responsible for the accelerated neoplastic process in young patients.

Impiego della spettrometria di massa nell'analisi di fumonisine in alimenti e matrici di origine animale

Mycotoxins are heterogeneous chemical compounds characterized by a low molecular weight and synthesized by the secondary metabolism of different molds. Fumonisins are water-soluble mycotoxins produced by Fusarium species spoiling corn and derived produc ts. These mycotoxins can be a health hazard when consuming contaminated cereals, but they can reach humans also indirectly through the consumption of food products derived from animals fed with contaminated feed. Fumonisins have been associated with several animal and human diseases: they are suspected risk factors for esophageal and liver cancers, neural tube defects and cardiovascular problems. Improved methods are needed to accurately assess fumonisins concentrations in food of vegetable and animal origin, in order to prevent acute and chronic human exposure. The aim of the present work was to evaluate the versatility and the performances of mass spectrometry, coupled with liquid chromatography, in fumonisins analysis from foods and matrices of animal origin. Different methods for the identification and quantification of fumonisins and related products have been developed and validated to determine fumonisin B1 in milk, fumonisin B1, fumonisin B2 and their complete hydrolyzed products (HFB1 and HFB2) in pig liver and fumonisins B1 and B2 in complete and complementary dry dog food. The experimental procedures have been carefully studied, considering matrices features, number and type of molecules to detect. Therefore, several extraction, clean up and separation techniques were tested in order to obtain the better conditions of sample processing. The fit for purpose sample preparation, matched with high mass spectrometry sensibility and specificity, have allowed to achieve good results in any tested animal matrices. Hence, the developed methods were validated and have shown a high accuracy, sensibility and precision, fulfilling performance requirements of Decision 2002/657/EC and of European Project Standard, Measuring and Testing (SMT). In any developed method, the analytes were identified and quantified even at very low concentrations : the limits of quantification resulted lower than other similar works, performed with different detectors. These methods were applied to some commercial samples and to some samples collected for research projects in the Department of Veterinary Public Health and Animal Pathology (DVPHAP) of University of Bologna. Although the disclosed data must be considered completely preliminary and without statistical significance, they emphasize the presence of mycotoxins in animal products. The outcomes obtained from the processed samples (bovine milk, pig liver and dry dog food) suggest the efficacy of these methods also on other food matrices, confirming the versatility and the performances of mass spectrometry, coupled with liquid chromatography, in fumonisins analysis. Moreover the results underline the need to set up a large scale monitoring in order to evaluate the presence of fumonisins in food of animal origin for human consumption.

Circoli collaterali porto-sistemici all'eco-color-Doppler addominale in pazienti con ipertensione portale cirrotica: correlazione con il gradiente porto-epatico e valore prognostico

Background. Abdominal porto-systemic collaterals (APSC) on Color-Doppler ultrasound are a frequent finding in portal hypertensive cirrhotic patients. In patients with cirrhosis, an HVPG ≥ 16mmHg has been shown to be associated with increased mortality in two studies. Non-invasive indicators of HVPG ≥ 16 mmHg might define a subgroup of high-risk patients, but data on this aspect are lacking. Aims. We aimed to investigate whether HVPG predicts mortality in patients with clinically significant portal hypertension, and if APSC may predict a severe portal hypertensive state (i.e. HVPG≥16mmHg) in patients with cirrhosis and untreated portal hypertension. Methods. We analysed paired HVPG and ultrasonographic data of 86 untreated portal hypertensive cirrhotic patients. On abdominal echo-color-Doppler data on presence, type and number of APSC were prospectively collected. HVPG was measured following published guidelines. Clinical, laboratory and endoscopic data were available in all cases. First decompensation of cirrhosis and liver-disease related mortality on follow-up (mean 28±20 months) were recorded. Results. 73% of patients had compensated cirrhosis, while 27% were decompensated. All patients had an HVPG≥10 mmHg (mean 17.8±5.1 mmHg). 58% of compensated patients and 82% of decompensated patients had an HVPG over 16 mmHg. 25% had no varices, 28% had small varices, and 47% had medium/large varices. HVPG was higher in patients with esophageal varices vs. patients without varices (19.0±4.8 vs. 14.1±4.2mmHg, p<0.0001), and correlated with Child-Pugh score (R=0.494,p=0.019). 36 (42%) patients had APSC were more frequent in decompensated patients (60% vs. 35%, p=0.03) and in patients with esophageal varices (52% vs. 9%,p=0.001). HVPG was higher in patients with APSC compared with those without PSC (19.9± 4.6 vs. 16.2± 4.9mmHg, p=0.001). The prevalence of APSC was higher in patients with HVPG≥16mmHg vs. those with HVPG<16mmHg (57% vs. 13%,p<0.0001). Decompensation was significantly more frequent in patients with HVPG≥16mmHg vs. HVPG<16mmHg (35.1% vs. 11.5%, p=0.02). On multivariate analysis only HVPG and bilirubin were independent predictors of first decompensation. 10 patients died during follow-up. All had an HVPG≥16 mmHg (26% vs. 0% in patients with HVPG <16mmHg,p=0.04). On multivariate analysis only MELD score and HVPG ≥16mmHg were independent predictors of mortality. In compensated patients the detection of APSC predicted an HVPG≥16mmHg with 92% specificity, 54% sensitivity, positive and negative likelihood ratio 7.03 and 0.50, which implies that the demonstration of APSC on ultrasound increased the probability of HVPG≥16mmHg from 58% to 91%. Conclusions. HVPG maintains an independent prognostic value in the subset of patients with cirrhosis and clinically significant portal hypertension. The presence of APSC is a specific indicator of severe portal hypertension in patients with cirrhosis. Detection of APSC on ultrasound allows the non-invasive identification of a subgroup of compensated patients with bad prognosis, avoiding the invasive measurement of HVPG.

Analisi proteomica dei meccanismi sottesi alla malatia da reflusso gastroesofageo

La malattia da reflusso gastroesofageo (GERD) si divide in due categorie: malattia non erosiva (NERD) ed erosiva (ERD). Questi due fenotipi di GERD mostrano caratteristiche patofisiologiche e cliniche differenti. NERD è la forma più comune. Anche se ERD e NERD sono difficili da distinguere a livello clinico, la forma NERD possiede caratteristiche fisiologiche, patofisiologiche, anatomiche, e istologiche uniche. La replicazione cellulare dello strato basale si pensa sia una delle cause implicate nella resistenza della mucosa e nella difesa strutturale dell’epitelio. Diversi studi hanno dimostrato che la proliferazione cellulare è ridotta nella mucosa esofagea esposta ad insulti acidi e peptici cronici, in pazienti GERD, in più uno studio recente ha dimostrato che il recettore per i cannabinoidi CB1 era implicato nella riparazione delle ferite nella mucosa del colon. Sulla base di questi dati abbiamo valutato la presenza del recettore CB1 in biopsie della mucosa esofagea, di pazienti ERD, NERD e di controlli sani, tramite analisi Western Blot, Immunoistochimica e Real-Time PCR, dimostrando per la prima volta la presenza di questo recettore nell’epitelio dell’esofago e una riduzione dei suoi livelli di espressione nei pazienti ERD, camparati con i NERD e con i controlli sani. Successivamente, per chiarire meglio i meccanismi molecolari che caratterizzano ERD e NERD, abbiamo effettuato un analisi proteomica con la tecnica shotgun, la quale ha evidenziato un patter proteico di 33 proteine differenzialmente espresse in pazienti NERD vs ERD, sette delle quali confermate in wester Blot, e quattro in immunoistochimica. Concludendo i nostri risultati hanno confermato che ERD e NERD sono due entità distinte a livello proteico, e hanno proposto dei candidati biomarker per la diagnosi differenziale di ERD e NERD.

Interspecies study of the enteric nervous system and related pathologies

The enteric nervous system (ENS) modulates a number of digestive functions including well known ones, i.e. motility, secretion, absorption and blood flow, along with other critically relevant processes, i.e. immune responses of the gastrointestinal (GI) tract, gut microbiota and epithelial barrier . The characterization of the anatomical aspects of the ENS in large mammals and the identification of differences and similarities existing between species may represent a fundamental basis to decipher several digestive GI diseases in humans and animals. In this perspective, the aim of the present thesis is to highlight the ENS anatomical basis and pathological aspects in different mammalian species, such as horses, dogs and humans. Firstly, I designed two anatomical studies in horses:  “Excitatory and inhibitory enteric innervation of horse lower esophageal sphincter”.  “Localization of 5-hydroxytryptamine 4 receptor (5-HT4R) in the equine enteric nervous system”. Then I focused on the enteric dysfunctions, including:  A primary enteric aganglionosis in horses: “Extrinsic innervation of the ileum and pelvic flexure of foals with ileocolonic aganglionosis”.  A diabetic enteric neuropathy in dogs: “Quantification of nitrergic neurons in the myenteric plexus of gastric antrum and ileum of healthy and diabetic dogs”.  An enteric neuropathy in human neurological patients: “Functional and neurochemical abnormalities in patients with Parkinson's disease and chronic constipation”. The physiology of the GI tract is characterized by a high complexity and it is mainly dependent on the control of the intrinsic nervous system. ENS is critical to preserve body homeostasis as reflect by its derangement occurring in pathological conditions that can be lethal or seriously disabling to humans and animals. The knowledge of the anatomy and the pathology of the ENS represents a new important and fascinating topic, which deserves more attention in the veterinary medicine field.

Terapia chirurgica dell'acalasia scompensata: prevalenza e fattori di rischio per lo sviluppo del carcinoma esofageo, risultati clinico-funzionali a lungo termine della chirurgia conservativa e dell'esofagectomia

La chirurgia conservativa o l’esofagectomia, possono essere indicate per il trattamento della disfagia nell’acalasia scompensata. L’esofagectomia è inoltre finalizzata alla prevenzione dello sviluppo del carcinoma esofageo. Gli obiettivi erano: a) definire prevalenza e fattori di rischio per il carcinoma epidermoidale; b) confrontare i risultati clinici e funzionali di Heller-Dor con pull-down della giunzione esofagogastrica (PD-HD) ed esofagectomia. I dati in analisi, ricavati da un database istituito nel 1973 e finalizzato alla ricerca prospettica, sono stati: a) le caratteristiche cliniche, radiologiche ed endoscopiche di 573 pazienti acalasici; b) il risultato oggettivo e la qualità della vita, definita mediante questionario SF-36, dopo intervento di PD-HD (29 pazienti) e dopo esofagectomia per acalasia scompensata o carcinoma (20 pazienti). Risultati: a) sono stati diagnosticati 17 carcinomi epidermoidali ed un carcinosarcoma (3.14%). Fattori di rischio sono risultati essere: il diametro esofageo (p<0.001), il ristagno esofageo (p<0.01) e la durata dei sintomi dell’acalasia (p<0.01). Secondo l’albero di classificazione, soltanto i pazienti con esito insufficiente del trattamento ai controlli clinico-strumentali ed acalasia sigmoidea presentavano un rischio di sviluppare il carcinoma squamocellulare del 52.9%. b) Non sono state riscontrate differenze statisticamente significative tra i pazienti sottoposti ad intervento conservativo e quelli trattati con esofagectomia per quanto concerne l’esito dell’intervento valutato mediante parametri oggettivi (p=0.515). L’analisi della qualità della vita non ha evidenziato differenze statisticamente significative per quanto concerne i domini GH, RP, PF e BP. Punteggi significativamente più elevati nei domini RE (p=0.012), VT (p<0.001), MH (p=0.001) e SF (p=0.014) sono stati calcolati per PD-HD rispetto alle esofagectomie. In conclusione, PD-HD determina una miglior qualità della vita, ed è pertanto la procedura di scelta per i pazienti con basso rischio di cancro. A coloro che abbiano già raggiunto i parametri di rischio, si offrirà l’esofagectomia o l'opzione conservativa seguita da protocolli di follow-up.

Pattern peristaltico uterino nell'adenomiosi isolata: studio prospettico

Obiettivi dello studio: valutare con l’ecografia transvaginale la peristalsi uterina in fase periovulatoria in donne con adenomiosi isolata, confrontandola con un gruppo di controllo e, secondariamente, valutare il grado di accordo tra gli sperimentatori nella descrizione dei pattern di contrattilità. Disegno dello studio: studio osservazione prospettico condotto presso il Policlinico S. Orsola- Malpighi di Bologna, Italia. Materiali e Metodi: sono state reclutate pazienti afferenti al Centro per valutazione ambulatoriale, suddivise sulla base dei criteri di inclusione ed esclusione nei gruppi A (adenomiosi) e B (controlli) e sono state sottoposte da un unico ecografista esperto a ecografia transvaginale con registrazione di un video della durata di 180 secondi della scansione sagittale dell’utero. La registrazione è stata rivalutata off line da due sperimentatori esperti ecografisti, non a conoscenza della storia clinica delle pazienti e in cieco l’uno rispetto all’altro, che hanno descritto il pattern contrattile. È stata stimata una numerosità campionaria di 18 pazienti per gruppo per ottenere una differenza del 20% nell’obiettivo primario con una significatività del 5% (power 80%). Risultati: di 51 pazienti reclutate nello studio, a seguito di drop out 36 sono state sottoposte alla videoregistrazione ecografica (18 per gruppo). Il pattern peristaltico nel gruppo A è risultato alterato in maniera statisticamente significativa rispetto al gruppo B con un p value= 0,02. Sono stati osservati un pattern retrogrado nel 27,8% vs 72,2%, anterogrado del 11,1% vs 16,7%, opposto 38,9% vs 5,6% e random nel 22,2% vs 5,6%, rispettivamente nel gruppo A e B. Il calcolo dell’accordo interosservatore ha portato a un κ value di 0,92. Conclusioni: l’adenomiosi isolata è associata a disperistalsi uterina, che concorrerebbe nello sviluppo dei sintomi tipici dell’adenomiosi. L’ecografia transvaginale rappresenta uno strumento accessibile e utile nella valutazione della contrattilità uterina in quanto il grado di accordo tra gli sperimentatori è ottimo.

Pathophysiology of bile acid aspiration in lung transplant recipients

Duodeno-gastroesophageal reflux aspiration is associated with chronic lung allograft dysfunction (CLAD) and aspiration of bile acids (BA), functional molecules in the gastro-intestinal tract with emulsifying properties. While links between reflux aspiration to lung disease have been identified, the relevance of bile acid as molecular ligands and outcome predictors is poorly defined. We sought to determine and quantify the various BA species in airways of the lung transplant recipients to better understand the various effects of aspirated BA that contribute to post-transplantation outcomes and to investigate their molecular effects on airway function and contractility.

Pathogenetic mechanisms of gastrointestinal symptoms in a mouse model of Fabry disease: insights on the microbiota-gut-brain axis

Fabry disease (FD), X-linked metabolic disorder caused by a deficiency in α-galactosidase A activity, leads to the accumulation of glycosphingolipids, mainly Gb3 and lyso-Gb3, in several organs. Gastrointestinal (GI) symptoms are among the earliest and most common, strongly impacting patients’ quality of life. However, the origin of these symptoms and the exact mechanisms of pathogenesis are still poorly understood, thus the pressing need to improve their knowledge. Here we aimed to evaluate whether a FD murine model (α-galactosidase A Knock-Out) captures the functional GI issues experienced by patients. In particular, the potential mechanisms involved in the development and maintenance of GI symptoms were explored by looking at the microbiota-gut-brain axis involvement. Moreover, we sought to examine the effects of lyso-Gb3 on colonic contractility and the intestinal epithelium and the enteric nervous system, which together play important roles in regulating intestinal ion transport and fluid and electrolyte homeostasis. Fabry mice revealed visceral hypersensitivity and a diarrhea-like phenotype accompanied by anxious-like behavior and reduced locomotor activity. They reported also an imbalance of SCFAs and an early compositional and functional dysbiosis of the gut microbiota, which partly persisted with advancing age. Moreover, overexpression of TRPV1 was found in affected mice, and partial alteration of TRPV4 and TRPA1 as well, identifying them as possible therapeutic targets. The Ussing chamber results after treatment with lyso-Gb3 showed an increase in Isc (likely mediated by HCO3- ions movement) which affects neuron-mediated secretion, especially capsaicin- and partly veratridine-mediated. This first characterization of gut-brain axis dysfunction in FD mouse provides functional validation of the model, suggesting new targets and possible therapeutic approaches. Furthermore, lyso-Gb3 is confirmed to be not only a marker for the diagnosis and follow-up of FD but also a possible player in the alteration of the FD colonic ion transport process.