The generic call for proposals from the ANR 2015 clearly encourages and supports integration of reliable,
multi-sourced data that, when efficiently analyzed, interpreted, disseminated and used, can become an almost
inexhaustible source of knowledge to fuel a learning healthcare system.
This is exactly the purpose of ProteoCardis which proposes an unprecedented intestinal metaproteome-wide
association study of coronary artery disease (CAD), where newly acquired huge metaproteomics data will be
put into perspective with patient records, metabolic features, complete cardio-vascular exams and outcomes
that are acquired in the FP7 MetaCardis framework and will be refined with the ANR’s support. The whole
process will be achieved in a structured and documented manner in order to produce a standard operating
procedures (SOPs) useful in this still unexplored but promising research field.
In the MetaCardis FP7 framework (2013-2017), the gut metagenomes of more than 2000 patients at different
stages of their cardiometabolic disease are being characterized by high throughput sequencing of the total
fecal DNA. This will provide an enormous reservoir for the discovery of unsuspected metagenomic
signatures that can represent predictive biomarkers and unsuspected new therapeutic targets for different
disease phenotypes or stages.
The accompanying challenge proposed here is a holistic metaproteomics approach to move beyond the
genetic potential addressed by metagenomics and get closer to the real functionality of the gut microbiome
by exploring the expression of metabolic and cellular pathways. Understanding how they are altered in
disease can have a profound impact on patient treatment and disease prevention. This may open new avenues
for reducing risk, including the discovery of new biomarkers, new targets and new therapeutic molecules.
ProteoCardis will follow a step-by-step approach that we have already successfully experienced on a modest
scale.
First, in a well-controlled shotgun metaproteomics approach, and without any a priori assumption of the
metabolic and/or cellular pathways that can accompany the disease, we will search for metaproteomic
variables that are associated with CAD in 50 patients with acute event and 100 patients with chronic
coronaropathy with or without congestive heart failure (CHF), compared to 50 healthy controls (CTRL)
matched with BMI and sex. The change of protein signals before and one year after bariatric surgery, an
intervention known to reduce the cardiovascular risk, will also be examined (two observation times in the
same 20 BS subjects). Finally, we will provide a set of relevant variables from those obtained in both
contexts of aggravation (CAD vs. CTRL) and improvement (BS2 vs. BS1) of the clinical status.
Then, to confirm the candidates and test their predictive value in high-risk patients, a multiplexed SRM
(selected reaction monitoring) assay will be developed, targeting and precisely quantifying those
proteins/peptides of interest. The validation process will be done by a recognized team in an independent
manner, first on a subset of 20 CAD patients and 20 matched controls. ProteoCardis will subsequently
examine the presence of these signals in 150 additional individuals at high risk of CAD (50 subjects with
metabolic syndrome, 50 obese and 50 type 2 diabetic subjects) and association of these signals with any risk
factors as well as complications or adverse cardiovascular outcomes of the patients over a four year period.
The expected results have two levels of impact: immediate, since the whole experiment as a Standard
Operational Procedure (SOP) will define new standards and share best practice among the scientific
community for quantitative metaproteomics; longer-term, by pioneering a new map of knowledge linking
together proteomic, metagenomic and clinical data related to CAD pathology, that will contribute to the
opening of new avenues for maintaining or restoring health.