IRCM Biomarker Pipeline

OVERVIEW OF THE PIPELINE

DISCOVERY

We privilege three technologies to identify proteins that change in response to disease conditions or as a result of disease-causative mutations:

• Protein affinity purification coupled with mass spectrometry (AP-MS with FLAG tag)

• Proximity-Dependent Protein Identification (BioID)

• Tandem Mass Tag Mass spectrometry (TMT-MS)

For examples, see:

Leukodystrophy-associated POLR3A mutations down-regulate the RNA polymerase III transcript and important regulatory RNA BC200

Choquet K, Forget D, Meloche E, Dicaire MJ, Bernard G, Vanderver A, Schiffmann R, Fabian MR, Teichmann M, Coulombe B, Brais B, Kleinman CL.

J Biol Chem. 2019;294(18):7445-7459.

Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III

Thiffault I, Wolf NI, Forget D, Guerrero K, Tran LT, Choquet K, Lavallée-Adam M, Poitras C, Brais B, Yoon G, Sztriha L, Webster RI, Timmann D, van de Warrenburg BP, Seeger J, Zimmermann A, Máté A, Goizet C, Fung E, van der Knaap MS, Fribourg S, Vanderver A, Simons C, Taft RJ, Yates JR 3rd,Coulombe B, Bernard G.

Nat Commun. 2015 Jul 7;6:7623.

The leukodystrophy mutation Polr3b R103H causes homozygote mouse embryonic lethality and impairs RNA polymerase III biogenesis

Choquet K, Pinard M, Yang S, Moir RD, Poitras C, Dicaire MJ, Sgarioto N, Larivière R, Kleinman CL, Willis IM, Gauthier MS, Coulombe B, Brais B.

Mol Brain. 2019 Jun 20;12(1):59.

VALIDATION

For the quantification of biomarkers in biological and clinical samples, we privilege a technology termed Protein Affinity Capture coupled with quantitative Mass Spectrometry (PAC-qMS). PAC-qMS can be operated at medium throughput (100s samples) and is ideal to quantify posttranslational modifications.

For examples, see:

Ser-Phosphorylation of PCSK9 (Proprotein Convertase Subtilisin-Kexin 9) by Fam20C (Family With Sequence Similarity 20, Member C) Kinase Enhances Its Ability to Degrade the LDLR (Low-Density Lipoprotein Receptor)

Ben Djoudi Ouadda A, Gauthier MS, Susan-Resiga D, Girard E, Essalmani R, Black M, Marcinkiewicz J, Forget D, Hamelin J, Evagelidis A, Ly K, Day R, Galarneau L, Corbin F, Coulombe B, Çaku A, Tagliabracci VS, Seidah NG.

Arterioscler Thromb Vasc Biol. 2019 Oct;39(10):1996-2013.

Posttranslational modification of proprotein convertase subtilisin/kexin type 9 is differentially regulated in response to distinct cardiometabolic treatments as revealed by targeted proteomics

Gauthier MS, Awan Z, Bouchard A, Champagne J, Tessier S, Faubert D, Chabot K, Garneau PY, Rabasa-Lhoret R, Seidah NG, Ridker PM, Genest J, Coulombe B.

J Clin Lipidol. 2018 Jul-Aug;12(4):1027-1038.

A semi-automated mass spectrometric immunoassay coupled to selected reaction monitoring (MSIA-SRM) reveals novel relationships between circulating PCSK9 and metabolic phenotypes in patient cohorts

Gauthier MS, Pérusse JR, Awan Z, Bouchard A, Tessier S, Champagne J, Krastins B, Byram G, Chabot K, Garneau P, Rabasa-Lhoret R, Faubert D, Lopez MF, Seidah NG, Coulombe B.

Methods. 2015 Jun 15;81:66-73.

ACTIVE PROJECTS

1. Unraveling the molecular basis of novel forms of hypomyelinating leukodystrophies (CIHR, Lead G. Bernard MUHC).

2. A biomarker discovery pipeline for precision medicine (Government of Quebec/IRCM, Lead B. Coulombe IRCM).

3. A patient-derived iPSC platform of disease relevant cell models for biological studies (ALS Canada and Brain Canada, Lead G. Rouleau The Neuro).

4. A machine learning approach to decipher protein-protein interactions in human plasma (IVADO and Genome Québec, Lead B. Coulombe IRCM).

5. Modulation of protein interactions by the Superoxide Dismutase 1 (SOD1) (supported by Atomwise Inc, Lead B. Coulombe IRCM).

6. The soluble fragment of neuroligin-1 as a blood biomarker of prodromal Alzheimer’s disease (Weston Brain Institute, Lead J. Brouillette HSCM).

7. Characterization of neuro-muscular junctions in ALS patients (ALS Canada, Lead R. Robitaille, U Montreal).

8. Reducing the activity of the phosphatase STEP to improve memory performance during aging (CIHR, Lead J. Brouillette HSCM).