“-Omic” technologies can detect the entirety of the molecules in the biological sample of interest, in a non-targeted and non-biased fashion. The integration of multiple types of omics data, known as “multi-omics” or “vertical omics”, can provide a better understanding of how the cause of disease leads to its functional consequences, which is particularly valuable in the study of complex diseases, that are caused by the interaction of multiple genetic and regulatory factors with contributions from the environment. In the present work appropriate multi-omics approaches are applied to two complex conditions that usually first manifest in childhood, have rising incidence and gaps in the knowledge of their molecular pathology, specifically Congenital Lung Malformations and Coeliac Disease. The aims are, respectively, to verify if cancer-associated genomic variants or DNA methylation features exist in the malformed lung tissue and to find common alterations in the methylome and the transcriptome of small intestine epithelial cells of children with CD. The methods used in the Congenital Lung Malformations project are Whole Genome Methylation microarrays and Whole Genome Sequencing, and for the Coeliac Disease the whole genome methylation microarrays and mRNA sequencing. Differentially methylated regions in possibly cancer-related genes were found in each one of the 20 lung malformation samples included. Moreover, 5 malformed samples had at least one somatic missense single nucleotide variant in genes known as lung cancer drivers, and 5 malformed samples had a total of 2 deletions of lung cancer driver tumour suppressor and 10 amplifications of lung cancer driver oncogenes. The data showed that congenital lung malformations can have premalignant genetic and epigenetic features, that are impossible to predict with clinical information only. In the second project, Principal Component Analysis of the whole genome methylation data showed that CD patients divide into two clusters, one of which overlaps with controls. 174 genes were differentially methylated compared to the controls in both clusters. Principal Component Analysis of gene expression data (mRNA-Seq) showed a distribution that is similar to the methylation data, and 442 genes were differentially expressed in both clusters. Six genes, mainly related to interferon response and antigen processing and presentation, were differentially expressed and methylated in both clusters. These results show that the intestinal epithelial cells of individuals with CD are highly variable from a molecular point of view, but they share some fundamental differences that make them able to respond to interferons, process, and present antigens more efficiently than controls. Despite the limitations of the present studies, they have shown that targeted multi-omics approaches can be set up to answer the relevant disease-specific questions by investigating many cellular functions at once, often generating new hypotheses and making unexpected discoveries in the process.
Le tecnologie “-omiche” studiano l’insieme delle molecole presenti nel campione biologico di interesse, in maniera completamente agnostica. L’integrazione di diversi tipi di dati omici, chiamata “multi-omica” o “omica verticale”, fornisce indicazioni importanti su come le cause di una malattia portano alle sue conseguenze funzionali. Queste indicazioni sono particolarmente utili nel caso delle malattie complesse, che sono causate dall’interazione di vari fattori genetici e regolatori con vari contributi ambientali. In questo lavoro, degli approcci multi-omici appropriati sono stati applicati a due malattie complesse che di solito iniziano a manifestarsi durante l’infanzia, hanno un’incidenza crescente, e hanno vari elementi sconosciuti nella loro patologia molecolare, ovvero le malformazioni polmonari congenite e la celiachia. Gli scopi dei due progetti sono, rispettivamente, di verificare se nel tessuto polmonare malformato ci sono varianti genetiche o alterazioni della metilazione del DNA associate al cancro, e di trovare alterazioni comuni nel metiloma e nel trascrittoma di cellule epiteliali dell’intestino tenue di bambini affetti da celiachia. Per quanto riguarda i metodi, nel progetto sulle malformazioni polmonari sono stati usati microarray di metilazione whole genome e sequenziamento dell’intero genoma, mentre nel progetto sulla celiachia sono stati usati microarray di metilazione whole genome e sequenziamento dell’mRNA totale. In tutte le 20 malformazioni polmonari incluse nello studio sono state trovate regioni differenzialmente metilate in geni probabilmente legati al cancro del polmone. Inoltre, 5 campioni malformati avevano almeno una variante somatica missenso in un gene noto come driver del tumore del polmone, e 5 altri campioni avevano un totale di 2 delezioni di oncosoppressori driver del tumore del polmone e 10 amplificazioni di oncogeni driver del tumore del polmone. Questi dati suggeriscono che le malformazioni polmonari congenite possono avere alterazioni genetiche ed epigenetiche di tipo pre-maligno, la cui presenza è impossibile da prevedere sulla base delle sole informazioni cliniche. Nel secondo progetto, una Principal Component Analysis dei dati di metilazione ha mostrato che i pazienti celiaci si dividono in due cluster, di cui uno si sovrappone ai controlli. 174 geni erano differenzialmente metilati rispetto ai controlli in entrambi i cluster. Una Principal Component Analysis dei dati di espressione genica (mRNA-Seq) ha mostrato una distribuzione simile a quella dei dati di metilazione, e 442 geni erano differenzialmente espressi in entrambi i cluster. Sei geni, principalmente coinvolti nella risposta interferonica e nel processo di processamento e presentazione degli antigeni, erano sia differenzialmente espressi che differenzialmente metilati in entrambi i cluster. Questi risultati indicano che le cellule epiteliali dell’intestino tenue di bambini affetti da celiachia sono altamente variabili da un punto di vista molecolare, ma condividono delle differenze fondamentali che le rendono in grado di rispondere agli interferoni e di processare e presentare antigeni con maggiore efficienza rispetto ai controlli. Nonostante le loro limitazioni, gli studi presentati mostrano che degli approcci multi-omici specifici possono essere usati per rispondere alle domande ancora aperte riguardo a diverse malattie, studiando più funzioni cellulari contemporaneamente e spesso portando anche alla generazione di nuove ipotesi e a scoperte inaspettate.
Multi-omics approaches to complex diseases in children / Patrizi, Sara. - (2022 Mar 25).
Multi-omics approaches to complex diseases in children
PATRIZI, SARA
2022-03-25
Abstract
“-Omic” technologies can detect the entirety of the molecules in the biological sample of interest, in a non-targeted and non-biased fashion. The integration of multiple types of omics data, known as “multi-omics” or “vertical omics”, can provide a better understanding of how the cause of disease leads to its functional consequences, which is particularly valuable in the study of complex diseases, that are caused by the interaction of multiple genetic and regulatory factors with contributions from the environment. In the present work appropriate multi-omics approaches are applied to two complex conditions that usually first manifest in childhood, have rising incidence and gaps in the knowledge of their molecular pathology, specifically Congenital Lung Malformations and Coeliac Disease. The aims are, respectively, to verify if cancer-associated genomic variants or DNA methylation features exist in the malformed lung tissue and to find common alterations in the methylome and the transcriptome of small intestine epithelial cells of children with CD. The methods used in the Congenital Lung Malformations project are Whole Genome Methylation microarrays and Whole Genome Sequencing, and for the Coeliac Disease the whole genome methylation microarrays and mRNA sequencing. Differentially methylated regions in possibly cancer-related genes were found in each one of the 20 lung malformation samples included. Moreover, 5 malformed samples had at least one somatic missense single nucleotide variant in genes known as lung cancer drivers, and 5 malformed samples had a total of 2 deletions of lung cancer driver tumour suppressor and 10 amplifications of lung cancer driver oncogenes. The data showed that congenital lung malformations can have premalignant genetic and epigenetic features, that are impossible to predict with clinical information only. In the second project, Principal Component Analysis of the whole genome methylation data showed that CD patients divide into two clusters, one of which overlaps with controls. 174 genes were differentially methylated compared to the controls in both clusters. Principal Component Analysis of gene expression data (mRNA-Seq) showed a distribution that is similar to the methylation data, and 442 genes were differentially expressed in both clusters. Six genes, mainly related to interferon response and antigen processing and presentation, were differentially expressed and methylated in both clusters. These results show that the intestinal epithelial cells of individuals with CD are highly variable from a molecular point of view, but they share some fundamental differences that make them able to respond to interferons, process, and present antigens more efficiently than controls. Despite the limitations of the present studies, they have shown that targeted multi-omics approaches can be set up to answer the relevant disease-specific questions by investigating many cellular functions at once, often generating new hypotheses and making unexpected discoveries in the process.File | Dimensione | Formato | |
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