Characterization of monogenic enteropathies

Résumé

Background: Mendelian mutations causing monogenic enteropathies are identified in an increasing number of genes and are responsible for either chronic inflammatory diseases (frequently called VEO-IBD for very early-onset inflammatory bowel diseases) or for congenital diarrheal disorders (CDD). Management of many patients with monogenic enteropathies requires difficult therapeutic decisions and heavy treatments, such as hematopoietic stem cell transplantation for VEO-IBD patients, or total parenteral nutrition and intestinal transplantation for CDD patients. Early molecular diagnosis is crucial to define the most pertinent treatment and increase life expectancy. During my thesis, I introduced in the laboratory big data management tool (e. g. online dedicated database) and applied next-generation sequencing tools (whole exome sequencing (WES) and targeted gene panel sequencing (TGPS)) to a cohort of patients suffering from monogenic enteropathies in order to characterize them phenotypically and genetically. Methods: My thesis was divided in 4 steps. In Step 1, patients (n=216 in January 2016, n=260 in August 2016) recruited through a French research protocol (Immunobiota, 12 centers) and European network (GENIUS, 33 centers) were phenotypically characterized through an online dedicated database. Following precise phenotyping, molecular diagnoses were obtained by Sanger sequencing of candidate genes suggested by functional tests in Step 2. Step 3 was the adaptation of WES for our cohort of patients (59 patients were sequenced in trio and 11 sequenced by themselves or in duo) and lastly, in Step 4, TGSP was designed and applied to our cohort (173 patients without a molecular diagnosis). Findings: The cohort gathered 57 patients including 22 with a molecular diagnosis in January 2012, and 216 patients including 70 with a diagnosis in January 2016, corresponding to a global diagnosis rate of 1/3. Approximately 50 new patients are recruited each year, with blood samples taken from each patient, both parents and siblings. During this period, 11 diagnoses were obtained by a phenotype-based approach, with identification of mutations notably in IL-10R (4 patients) and XIAP (4 patients). Eleven patients obtained a genetic diagnosis by WES including two siblings with a MALT1 deficiency responsible for an IPEX-like syndrome. Because of the increasing number of genes involved in monogenic enteropathies, we developed, in collaboration with Genomics, Bioinformatics and Translational Genetics platforms from the Institut IMAGINE, a custom-made TGPS gathering 68 genes responsible for either VEO-IBD or CDD. The sequencing of all negative patients (n=173) on this panel allowed to identify 28 new diagnoses (among which 8 were made in patients included before 2012). Interpretation: This work lead to the identification of the genetic diagnosis in 1/3 patients. The close investigations of phenotype-genotype correlations highlighted frequent overlaps among monogenic enteropathies. Following completion of this work, we suggest to use TGPS as a first-line genetic test in addition to a precise phenotyping of the patient. Depending on the results, TGPS will either reach an early molecular diagnosis crucial to optimize treatments in a cost-effective manner, or allow to perform further genetic analysis notably by WES.

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