Study of expression levels in MECP2 related disorders using transcriptomics and proteomics: characterizing Rett syndrome and MECP2 duplication syndrome

Abstract

[eng] MECP2 is a multifunctional gene involved in multiple processes such as transcription regulation, chromatin remodelling, splicing and miRNA regulation. Malfunction of MECP2 due to loss of function mutations leads to Rett syndrome (RTT) whereas its overexpression triggers MECP2 duplication syndrome (MDS). Besides, variants in MECP2 can cause a wide spectrum of phenotypes, from severe congenital encephalopathy with early death to mild intellectual disability (ID). RTT and MDS are two well characterized rare diseases with a partly overlapping phenotype consisting of neurodevelopmental delay, ID, impaired muscle tone, lack or unstable ambulation, little or absent speech, gastrointestinal problems, autism like behaviour and hand stereotypies. With next generation sequencing derived methodologies, gigantic breakthroughs have been done in diagnostics and research. These new omic strategies, such as transcriptomic or proteomic, can be applied to patient-derived samples to obtain answers to some of the still unknown aspects of the molecular effect of MECP2 in RTT and MDS. For the present thesis project, patients with alterations in MECP2 were gathered and three cohorts were created and thoroughly studied and characterized: a classic RTT girls group with large deletions within MECP2, a group of patients with MDS together with their duplication carrier mothers, and a group of boys with ID and neurodevelopmental delay with variants in MECP2. Genotype-phenotype correlations were also attempted for these cohorts.

In order to further study patients with classic RTT and MDS we decided to use a multi-omic (transcriptomic and proteomic) approach. For that, 22 classic RTT, 17 MDS, 10 MECP2 duplication carriers and 13 healthy controls were gathered and primary cultured cell lines were established from their skin biopsies. DNA, RNA and proteins were extracted from them all and RNA sequencing and tandem mass tag-mass spectrometry (TMT-MS) experiments were performed. The obtained data was analysed in a case-control approach.

The multi-omic analysis revealed shared and distinct altered biological processes for each cohort studied. The gene causing RTT and MDS is the same, but its downstream molecular effects might be opposite. Being able to obtain RNA and protein profiles from these patient cohorts seems to be a promising way to better understand MECP2’s role in the underlying pathomechanism triggering RTT and MDS. Differentially expressed genes and proteins involved in cytoskeleton, vesicular activity or immune system were found, and some of them are highlighted as potential biomarker and therapeutic target candidates. Altogether, we aimed to fill the gap by exploring the patients’ genetics, transcriptomics and proteomics in order to get closer to identifying therapeutic targets and biomarkers that could be used in future clinical trials.