Aptamer- based proteomic profiling for predic?ng early mortality in heart failure pa?ents

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1 Aptamer- based proteomic profiling for predic?ng early mortality in heart failure pa?ents 2016 SomaLogic, Inc. Florence Pinet, Inserm UMR1167, Univ Lille, Ins?tut Pasteur de Lille, Lille - FRANCE florence.pinet@pasteur- lille.fr 1

2 Objective Find new biomarkers associated with early cardiovascular mortality in heart failure by a multi-marker approach 2

3 Characteris?cs of SOMAmer reagents 3

4 Using modified DNA to bind proteins SOMAmer reagents Slow Off- rate Modified Aptamer (SOMAmer) A new class of single strand DNA binding reagents Platelet- derived growth factor (PDGF) Modified DNA- based reagents (50 bp) selected to?ghtly bind their specific protein targets for a prolonged period of?me Nerve growth factor (NGF) Interleukin- 6 4

5 SOMAmer affinity reagents 5

6 Principle of SOMAscan 6

7 Summary of SOMAscan 7

8 SOMAscan (step 1) SOMAmers are pre- immobilized to beads Proteins (sample) introduced into each well Proteins complex to the SOMAmers 8

9 SOMAscan (step 2) Proteins are bio?nylated The photo- cleavable link is broken by exposure to ultra- violet light 9

10 SOMAscan (step 3) Non- speciﬁc complexes fall apart quickly Speciﬁc complexes stay together (slow oﬀ- rate) Second immobiliza?on step on new beads Unbound SOMAmers washed away 10

11 SOMAscan (step 4) SOMAmers eluted oﬀ the complexes # SOMAmers = # protein complexes DNA SOMAmers hybridized Fluorescence = # SOMAmers 11

12 SOMAscan (step 5) Hybridiza?on on Agilent arrays gives high dynamic range and excellent precision Every protein has its own standard curve 10 randomly placed spots averaged per protein A protein signal has been transformed into a DNA signal 12

13 SOMAscan analytics Measure simultaneously 1310 proteins Sample volume Broad dynamic range : 65 microliters (~8 logs) Very sensitive (median LOD ~1 pg/ml) High precision (median CV <5%) Throughput of hundreds of samples/day/ instrument system Specific for individual proteins 13

1 ug/ml 1 g/l 10 g/l Complexity of plasma proteome Plasma proteome Apo- A1 C3 cplt Haptoglobin IgM total IgA total α2 macroglobulin Transferrin C8 cplt C1q cplt C9 cplt Cplt factb Prealb Factor H C4

14 1 ug/ml 1 g/l 10 g/l Complexity of plasma proteome Plasma proteome Apo- A1 C3 cplt Haptoglobin IgM total IgA total α2 macroglobulin Transferrin C8 cplt C1q cplt C9 cplt Cplt factb Prealb Factor H C4 cplt Hemoglobin α- 1 acid GP total IgG Lp(a) Apo- B α1 an?trypsin Deep proteome Fibrinogen TIMP- 4 CX3CL1 MMP- 1 Apelin MMP- 8 PIIINP CXCL- 1 VEGF sfasl BNP Granzyme B CXCL10 Cardiac proteins CCL11 CCL13 ANP CCL4 CCL19 CXCL16 CCL2 CXCL12 NE HGF CCL5 t- PA AVP END I TNFα CXCL8 IL6 GM- CSF CCL3 ATII Nt- probnp CCL18 CCL21 sst2 sfas HMGB1 MMP- 7 ICTP 1 pg/ml 1 ng/ml Albumin PICP TIMP- 2 Tenascin- C MPO MMP- 3 Osteopon?n CXCL7 MMP- 2 TIMP- 1 MMP- 9 CRP Adiponec?n 1 μg/ml Fer?n et al, Am J Cardiol (2012) 14

15 SOMAscan assay dynamic range 15

16 Objectives of the use of SOMAscan 16

17 Aim Heart failure study Investigate protein biomarkers for risk stratification in heart failure Design: Compare protein signals in plasma from INCA study heart failure patients who were alive or dead within 3 years after study enrollment 84 controls, alive 84 dead of cardiovascular causes 17

18 Characteristics of INCA population 18

19 Reduced Ejection Fraction Heart Failure cohort : INCA From November 1998, prospective register including consecutively Heart failure patients (systolic HF with LVEF 45%) clinically stable => no decompensation, no hospitalization in the previous 2 months with an optimal medical therapy and, undergo a prognostic evaluation 19

20 Prognostic evaluation in INCA cohort This prognostic evaluation includes evaluation of the main prognostic markers of HF such as : NYHA class, BNP levels, LVEF measurement, Peak VO 2 obtained during cardiopulmonary exercise testing, All patients had a coronarography for determining etiology of cardiopathy 20

21 INCA population Cardiac death (cases, n=84) No cardiac death (controls, n=84) P value Age (yrs) 58.7 ± ± 10.2 na Gender (M/F) 78/6 78/6 na HF e?ology na Ischemic Non ischemic Diabetes mellitus NYHA class LV ejec?on frac?on (%) Peak VO 2 (ml/min/ kg) BNP* Low Intermediate High ± ± ± ± 4.7 4E Crea?nine (mg/l)** 12.6 ± ± Treatment at inclusion ACE inhibitors Beta- blockers Diure?cs

22 Design of SOMASCAN analysis Compare protein signals in plasma from INCA study heart failure participants who were alive or dead within 3 years after study enrollment 84 controls, alive 84 dead of cardiovascular causes 22

23 Process of the data 23

24 Analyses Plasma samples were analyzed with SOMAscan 1.3k assay, measuring 1,310 proteins Data were normalized and calibrated by SomaLogic standard procedures, then log10 transformed 4 samples (all controls) failed SOMAscan QC criteria and were excluded from the analysis Sample assessment hemolysis, kidney effect 24

25 Sample Quality is Good Hemolysis is assessed by comparing the SOMAscan hemoglobin vs haptoglobin levels Most samples fall into the expected, high quality sample values (low hemoglobin, high haptoglobin) 25

26 No Obvious Kidney Effect Between Groups Difference in kidney func?on between groups might have been expected as a consequence of heart failure severity Changes in egfr can alter the level of hundreds of serum/plasma proteins This effect was not seen: Cysta?n C measured by SOMAscan and crea?nine measured at CHRU of Lille show no difference between groups 26

27 Summary of SOMAscan data 27

28 BNP SOMAmer Correlation with Clinical BNP low intermediate high BNP decile 28

29 Analyses Biomarker analysis: 2 group comparisons (control/dead), applying false discovery rate correction, beginning with previously identified CV risk proteins CV 16: top prognostic proteins identified by Lasso CV200: top univariate prognostic proteins plus clinical variables All 1310 proteins plus clinical variables 29

30 CV200 and CHF Survival Test of 200 proteins linked to CV risk in patients with stable CHF in previous studies plus 5 clinical factors Clinical factors = age, BNP decile, creatinine, LVEF, peak VO 2 27 of these variables were significant by the KS test at FDR p< proteins, consistent with previous results 11 higher, 14 lower with increased risk 2 clinical variables: Peak VO 2 and BNP decile 6 proteins associated with RAP1 signaling pathway in larger set of 38 proteins FDR p<0.1 30

31 SOMAscan 1.3k Results 345 proteins and 2 clinical variables significant at KS test FDR p<0.05 Includes significant proteins from CV200 analysis Peak VO 2 drops to #132, BNP decile drops to #275 Enriched for cytokine ac?vity, inflamma?on, apoptosis 31

32 Summary SOMAscan analysis found proteins associated with poor outcome in heart failure patients Sample quality passed QC criteria Kidney effects did not explain group differences, egfr did not confound results Many previously identified markers of CV risk were associated with poor outcome in this study All significant proteins in this study moved in the expected direction for risk prediction and prognosis This approach may reveal new biomarkers and pathways to explore 32

33 Next step 33

34 Next step: system biology analysis Molecular interaction network analysis Building a multivariate model Subgroup analysis: ischemic vs non ischemic patients Integrative analysis of clinical and molecular data 34

35 Thank you 35

36 Florence Pinet, Inserm UMR1167, Univ Lille, Institut Pasteur de Lille, Lille -FRANCE 36

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