Multi-Omics and IPSCs to Improve Diagnosis of Rare Intellectual Disabilities (MIDRID)

Multi-Omics and IPSCs to Improve the Diagnosis of Rare Intellectual Disabilities

Background Genetic factors play a major role in intellectual disability (ID) but the underlying cause is not determined in many cases.

This proposal is the continuation of the previous interregional project HUGODIMS, the aim of which was to perform whole exome sequencing (WES) in 69 thoroughly selected simplex ID parent-child trios. Thanks to HUGODIMS consortium, the underlying genetic cause of ID was determined or highly suspected in 48 cases (69.5%) and 7 novel ID genes were identified.

Hypothesis Investigators hypothesize that an approach combining genomics, transcriptomics, metabolomics and morphological analyses performed on induced pluripotent stem cell (iPSC)-derived neural cells would improve diagnosis of ID. The current proposal is therefore a proof-of concept project aiming at assessing the relevance and effectiveness of this multi-omics approach.

Aims and Methods Ten individuals with ID recruited through HUGODIMS, in whom WES have failed to identify pathogenic variants will be included.

The workflow is the following:

1. Whole genome sequencing (WGS) (Nantes) of these 10 negative trios.
2. Bio-informatics analyses

3. In 3 WGS negative cases, 3 positive controls bearing distinct mutations in CAMK2a (a novel ID gene identified thanks to HUGODIMS), and 3 healthy negative controls:

   1. Derivation of induced pluripotent stem cell (iPSC)-derived neural progenitors (iPSC core facility at Nantes)
   2. Targeted and non-targeted metabolomics analyses performed on iPSC-derived neuronal cells (Angers)
   3. RNA sequencing performed on the 9 cell lines (Rennes)
   4. Morphological analyses of differentiated neuronal cell lines derived from 3 affected individuals and 3 positive controls bearing CMK2a mutations (Tours)
   5. Integration and validation of data from multi-omics and morphological approaches

Expected results and impact Investigatrors expect that this approach combining multi-omics and iPSC will help to improve diagnosis and understanding of genetic ID of unknown cause

Study Overview

• Status: Unknown
• Conditions: Rare Intellectual Disabilities
• Intervention / Treatment: Other: Blood sample

• Study Type: Interventional
• Enrollment (Anticipated): 6
• Phase: Not Applicable

Contacts and Locations

• Study Contact: Name: Dominique BONNEAU; Phone Number: 0241353883; Email: dobonneau@chu-angers.fr
• Study Contact Backup: Name: Dominique BONNEAU; Phone Number: 0241353883

Study Locations

• France
  • Angers, France
    • Not yet recruiting
    • Chu Angers
    • Contact: Dominique Bonneau
  • Bron, France
    • Recruiting
    • HCL LYON
    • Contact: Gaetan Lesca
  • Dijon, France
    • Not yet recruiting
    • CHU de Bourgogne
    • Contact: Anne-Sophie Denommée-Pichon
  • Nantes, France
    • Completed
    • CHU Nantes
  • Poitiers, France
    • Completed
    • CHU Poitiers
  • Rennes, France
    • Completed
    • CHU Rennes

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 2 years to 25 years (Child, Adult)
• Accepts Healthy Volunteers: No
• Genders Eligible for Study: All

Description

Inclusion Criteria:

• 3 Whole Genome Sequencing negative cases
• 3 positive controls bearing distinct mutations in CAMK2a

Exclusion Criteria:

• no informed consent/refusal

Study Plan

How is the study designed?

Design Details

• Primary Purpose: Diagnostic
• Allocation: N/A
• Interventional Model: Single Group Assignment
• Masking: None (Open Label)

Number of Arms

1

Arms and Interventions

Participant Group / Arm	Intervention / Treatment
Experimental: Blood sample; Blood sample for analyses	Other: Blood sample; combining genomics, transcriptomics, metabolomics and morphological analyses performed on induced pluripotent stem cell (iPSC)-derived neural cells

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
To evaluate the relevance and effectiveness of a multi-omics approach to the diagnosis of ID of unknown genetic origin.	Whole genome sequencing : de novo variants in non-coding regions of the genome, WGS will be performed using the HiSeq X Five System 5; Bionformatics analysis of WGS data; neuronal progenitors derived from iPSC	Day 1

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
The assessment of metabolomics consequences of CAMK2a mutations in human neuronal progenitors and differentiated neuronal cell lines	Coupled to high-resolution mass spectrometry ; Transcriptomics analyses: quality of the RNA will be evaluated with the Bioanalyzer (Agilent) on the basis of the RIN (RNA integrity number) as well as by taking into account the DV200, i.e. the percentage of RNA fragments with more than 200 nucleotides Non-targeted metabolomic analyses will be performed using a method based on ultra-high-performance liquid chromatography Flow injection analysis-tandem mass spectrometry for quantifying acylcarnitines, glycerophospholipids, sphingolipids and sugar, whereas liquid chromatography	Day 1
The assessment of morphological consequences of CAMK2a mutations in human neuronal progenitors and differentiated neuronal cell lines	immunocytochemistry and protein expression approaches using confocal microscopy and Western blotting with antibodies specific for proteins expressed in neurons (MAP2, Tubulin beta 3, PSD95, SNAP25), astrocytes (GFAP) or oligodendrocytes (Gal-C)	Day 1

Collaborators and Investigators

• Sponsor: University Hospital, Angers

Study record dates

Study Major Dates

• Study Start (Actual): January 9, 2019
• Primary Completion (Anticipated): March 1, 2020
• Study Completion (Anticipated): March 1, 2020

Study Registration Dates

• First Submitted: August 10, 2018
• First Submitted That Met QC Criteria: August 14, 2018
• First Posted (Actual): August 17, 2018

Study Record Updates

• Last Update Posted (Actual): January 3, 2020
• Last Update Submitted That Met QC Criteria: January 2, 2020
• Last Verified: January 1, 2020

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Mental Disorders; Nervous System Diseases; Neurologic Manifestations; Neurobehavioral Manifestations; Neurodevelopmental Disorders; Intellectual Disability
• Other Study ID Numbers: 49RC17_0224

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No