Biomarkers of Brain Disorders: from proteomics discovery to benchside
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1 Structural Biology and Bioinformatics Dpt Faculty of Medicine Biomarkers of Brain Disorders: from proteomics discovery to benchside Proteomica Clinica, A Coruna September 18 th, 2009
2 Talk Outlines I. Proteomics strategies for the discovery of brain damage markers II. Diagnosis of Ischemic stroke patients III. Prognosis of Subarachnoid hemorhage patients IV. From single analytes to panels
3 Does proteomics bridge discovery to clinics? Proteomics strategies are perfect for translational research, but PubMed search: Proteom* AND Diagno* vs. number of FDA-approved diagnostic markers FDA markers Number of publications FDA markers Number of publications
4 WHY? Most of the biomarkers were not specific enough or did not prove their clinical utility. Poor experimental study design. Validation difficult in the multicentric study phase. For diagnostic companies the payoff has never been really big. Most of the biomarkers are still under validation.
5 Are the biomarkers still under validation? Analytes Discovered FDA Commercialised Timing approved (Years) PSA Troponin BNP D-dimer S100b GFAP >30
6 Talk Outlines I. Proteomics strategies for the discovery of brain damage markers II. Diagnosis of Ischemic stroke patients III. Prognosis of Subarachnoid hemorhage patients IV. From single analytes to panels
7 Discovery of brain damage markers: Why? Several proteins synthesized in astroglial cells or neurons have been proposed as markers of central nervous system cell injury in the serum or in the cerebrospinal fluid. CK-BB, S100b, GFAP, NSE, tau, MBP,.. Not specific and sensitive enough to be used in clinical practice. The Clinical Problem: There is a need of new reliable blood markers to assist for the diagnosis and/or prognosis of braindamage disorders.
8 Discovery phase: Which sample? HIGH Specificity Brain tissue Pathology Convenience Biological context Brain fluids Neighbouring fluid Abundance Invasiveness LOW Plasma Diagnosis
9 Discovery phase: Which sample? HIGH Specificity Cerebrospinal fluid (CSF) Convenience Biological context Brain neighbouring fluids Abundance Invasiveness Brain interstitial fluid (ISF) LOW
10 Discovery phase: Which sample? Brain neighbouring fluids Brain interstitial fluid (ISF) Cerebrospinal fluid (CSF) Stroke patients Probe with mm a length of mm with a semi-permeable membrane at the tip. Perfusion at µl min -1 Infarct Core (IC) Contralateral (CT)
11 Ante- vs. post-mortem CSF using TMT labeling CSF MARS depletion Spiking of a bovine protein AM CSF 1 AM CSF 2 AM CSF PM CSF 1 PM CSF 2 PM CSF Concentration & buffer exchange Reduction, Alkylation Trypsin digestion TMT labeling Brain Interstitial Fluid Spiking of a bovine protein Pooling of the samples Off-Gel Electrophoresis RP-LC MS/MS Dayon et al Anal. Chem, Apr 15;80(8):
12 Ante- vs. post-mortem CSF using TMT labeling CSF MARS depletion Spiking of a bovine protein AM CSF 1 AM CSF 2 AM CSF PM CSF 1 PM CSF 2 PM CSF Concentration & buffer exchange Reduction, Alkylation Trypsin digestion TMT labeling 172 post-mortem CSF biomarkers Brain Interstitial Fluid Spiking of a bovine protein Pooling of the samples Off-Gel Electrophoresis RP-LC MS/MS Dayon et al Anal. Chem, Apr 15;80(8):
13 MS vs. ELISA-based verification MS-based quantification Relative abundance S100B Relative abundance GFAP Relative abundance PARK AM CSF PM CSF Ratio PM/AM = p < AM CSF PM CSF Ratio PM/AM = 8.44 (p = ) AM CSF PM CSF Ratio PM/AM = (p < 0.001) Conc ug/l b AM CSF S100B PM CSF Ratio PM/AM = p = Conc ug/l Dayon et al Anal. Chem, Apr 15;80(8): a AM CSF GFAP GFAP PM CSF Ratio PM/AM = 9.52 (p = ) Conc ug/l c PARK7 AM PM Ratio PM/AM = (p = ) ELISA verification
14 Infarct vs. controlateral ISF using TMT labeling CSF MARS depletion Spiking of a bovine protein 6 x Duplex TMT experiment Infarct ISF 1 Control ISF Concentration & buffer exchange Reduction, Alkylation Trypsin digestion TMT labeling Brain Interstitial Fluid Spiking of a bovine protein Pooling of the samples Dayon et al MCP, submitted. Off-Gel Electrophoresis RP-LC MS/MS
15 Infarct vs. controlateral ISF using TMT labeling CSF MARS depletion Spiking of a bovine protein 6 x Duplex TMT experiment Infarct ISF 1 Control ISF Concentration & buffer exchange Reduction, Alkylation Trypsin digestion TMT labeling Brain Interstitial Fluid Spiking of a bovine protein 88 brain infarct biomarkers Pooling of the samples Dayon et al MCP, submitted. Off-Gel Electrophoresis RP-LC MS/MS
16 Discovery of brain damage markers Brain neighbouring fluids Brain interstitial fluid (ISF) Cerebrospinal fluid (CSF) 88 brain infarct biomarkers 172 post-mortem CSF biomarkers Dayon et al MCP, submitted 210 potential brain damage biomarkers
17 Identified Potential Brain Markers GFAP, S100B, CK-BB,... NDKA (Nucleoside DiPhosphate Kinase A) PARK7 (DJ-1/ RNA-BP) UFD-1 (Ubiquitin Fusion degradation protein 1) H-FABP (Heart- Fatty Acidic Binding Protein)
18 Talk Outlines I. Proteomics strategies for the discovery of brain damage markers II. Diagnosis of Ischemic stroke patients III. Prognosis of Subarachnoid hemorhage patients IV. From single analytes to panels
19 What is a stroke? Cerebral Vascular Accidents : an interruption of the blood supply to the brain Hemorrhagic stroke Rupture of a vessel Bleeding disorders Arterial hypertension Aneurysms 20% 80% Ischemic stroke Clogging of a vessel Atherosclerosis Embolus Region of decreased blood flow Hemorrhage/ blood leaks into brain tissue Clot stops blood supply to an area of the brain If symptoms and lesions < 24 hours: transient ischemic attack (TIA).
20 Stroke Epidemiology In Spain and any industrialized countries : 3 rd cause of death 1 st cause of serious long term disabilities Age Race Incidence Sex Each year, people suffer a stroke in Spain : 1/3 die, 1/3 disability and 1/3 good recovery
21 Stroke diagnosis At the admission: Physician evaluation Sudden trouble seeing in one or both eyes Suspicion of stroke Brain Imaging Sudden, severe headache Sudden weakness or numbness of the face (but also arm or leg) Sudden confusion, trouble speaking or understanding CT-Confirmed Haemorrhagic stroke (high Sensitivity) Exclusion of stroke mimics?? (tumor, seizure, hypoglycemia, ) Ischemic stroke? Early diagnosis not Always possible Preventive anti-thrombotic treatment >24 hrs : MRI 3 days: scanner
22 Demographic Data Swiss Study (1) Swiss Study (2) Spanish study American study (1) American study (2) n Ischemic Hemorrhagic TIA n Ischemic Hemorrhagic TIA n Ischemic Hemorrhagic TIA n Ischemic Hemorrhagic TIA n Ischemic Hemorrhagic TIA Stroke Control TOTAL
23 DJ-1/PARK7 Swiss cohort North American 1 cohort North American 2 cohort control stroke (35) (35) Non parametric Wilcoxon matched-pairs test p< control stroke (30) (53) Mann-Whitney test p< 0.01 (100) (226) (183) (124) One-way ANOVA,Kruskal-Wallis test p< Swiss cohort (1) Spanish cohort North American 1 cohort North American 2 cohort control stroke (31) (31) Non parametric Wilcoxon matched-pairs test p< control stroke (29) (39) Mann-Whitney test p< Allard L et al., Clin.Chem. 2005, 51(11) : control stroke (30) (51) Mann-Whitney test p< 0.01 (99) (221) (183) (119) One-way ANOVA, Kruskal-Wallis test NDKA p< (Nucleoside DiPhosphate Kinase A)
24 DJ-1/PARK7 Swiss cohort North American 1 cohort North American 2 cohort control stroke (35) (35) Non parametric Wilcoxon matched-pairs test p< control stroke (30) (53) Mann-Whitney test p< 0.01 (100) (226) (183) (124) One-way ANOVA,Kruskal-Wallis test p< Swiss cohort (1) Spanish cohort North American 1 cohort North American 2 cohort control stroke (31) (31) Non parametric Wilcoxon matched-pairs test p< control stroke (29) (39) Mann-Whitney test p< Allard L et al., Clin.Chem. 2005, 51(11) : control stroke (30) (51) Mann-Whitney test p< 0.01 (99) (221) (183) (119) One-way ANOVA, Kruskal-Wallis test NDKA p< (Nucleoside DiPhosphate Kinase A)
25 Concentration as a function of time DJ1/PARK7 NDKA control vs. 0-3 h p<0.01 n=35 n=14 n=18 n=31 n=13 n=16 Evolution of the mean concentration for 3 months PARK7 NDKA N=119 6h 48h 6h 48h Allard L et al., Clin.Chem. 2005, 51(11) :
26 Talk Outlines I. Proteomics strategies for the discovery of brain damage markers II. Diagnosis of Ischemic stroke patients III. Prognosis of Subarachnoid hemorhage patients IV. From single analytes to panels
27 Prognosis of Aneurysmal Subarachnoid hemorrhage Sub-type of stroke mainly due to ruptured aneurysms 1/ people each year Relative young patients Diagnosis with evidence of bleeding in CT and presence of aneurysm at cerebral angiography Neurological scores: unique tools available for prognosis The Clinical Problem: Death or dependence (poor outcome) in almost 40% of patients Need of reliable predictors to assist for the prognosis of long-term neurological outcome
28 Prognosis of Subarachnoid Hemorrhage Goal: Focus attention on patients at risk of poor outcome after SAH How: Predicting long-term functional outcome in patients with severe SAH by the assessment of protein levels and clinical scores versus outcome after 6 months (GOS) Research cohort (training set): 19 Good outcome at 6 months (GOS 4-5) - 68% 9 Poor outcome at 6 months (GOS 1 to 3) - 32% Validation cohort (test set): 72 Good outcome at 6 months (GOS 4-5) - 64% 40 Poor outcome at 6 months (GOS 1 to 3) - 36% Evaluated parameters (17): Clinical: Age, neurological scores, location, presence of vasospasm, lung edema, hydrocephalus,.... Laboratory: S100b, Troponin I, H-FABP, NDKA, UFD1, PARK7.
29 Evaluation of 8 clinical parameters 1st set 2nd set GOS (N=9) GOS 4-5 (N=19) p GOS (N=40) GOS 4-5 (N=72) p Gender n% n% 3 (33.3) 6 (66.4) 5 (26.3) 14 (73.7) NS 19 (47.5) 21(52.5) 22(30.6) 50(69.4) NS Age (years) Median (range) Mean (± SD) 56 (49-75) 56.9 (±7.4) 57 (26-84) 53.5 (± 14.1) NS 54.5 (31-81) 54.9 (± 13.5) 49.5 (18-76) 48.9 (± 13.8) WFNS score 1-2 n% n% 4 (44.4) 5 (55.6) 18 (94.8) 1 (5.2) (32.5) 27 (67.5) 57 (79.2) 15 (20.8) <.0001 Fisher score 1-2 n% n% 0 (0) 9 (100) 5 (26.3) 14 (73.8) NS 0 (0) 40 (100) 19 (26.4) 53 (73.6) <.0001 Vasospasm No n% Yes n% 6 (66.7) 3 (33.3) 18 (94.8) 1 (5.2) NS 28 (70) 12 (30) 52 (72.2) 20 (27.3) NS Location* MCA n% CA n% ICA/PCA n% VBS n% 3 (33.3) 3 (33.3) 3 (33.3) 0 1 (5.2) 10 (52.7) 7 (36.9) 1 (5.2) NS 12 (30) 19 (47.5) 9 (22.5) 0 11 (15.3) 36 (50) 23 (31.9) 2 (2.8) NS Treatment No n% Coiling n% Surgery n% 1 (11.1) 6 (66.7) 2 (22.2) 0 18 (94.8) 1 (5.2) NS 2 (5) 28 (70) 10 (25) 2 (2.8) 60 (83.3) 10 (13.9) NS Seizures No n% Yes n% 6 (66.7) 3 (33.3) 13 (68.4) 6 (31.6) NS 32 (80) 8 (20) 58 (80) 14 (19.4) NS Turck N. et al., 2009 Intensive Care Medicine, in press.
30 4 brain-damaged and 1 cardiac biomarkers 1st Set 2nd Set GOS (N=9) GOS 4-5 (N=19) p GOS (N=40) GOS 4-5 (N=72) p H-FABP (µg/l) Median (range) Mean (± SD) 4.6 ( ) 12.1 (± 19.2) 1.8 ( ) 2.8 (± 2.1) ( ) 10.6 (± 16.4) 1.3 (0-44.4) 3.5 (± 7.3) <.0001 S100B (µg/l) Median (range) Mean (± SD) 0.3 ( ) 0.3 (± 0.1) 0.1 ( ) 0.2 (± 0.8) ( ) 0.4 (± 0.4) 0.1 ( ) 0.2 (± 0.1) <.0001 Troponin I (µg/l) Median (range) Mean (± SD) 0.5 ( ) 1.9 (± 2.5) 0.05 ( ) 1.1 (± 3.2) ( ) 5.6 (± 24.8) 0.05 ( ) 0.3 (± 0.8) <.0001 NDKA (µg/l) Median (range) Mean (± SD) 13.7 (0-46.4) 15.6 (± 13.8) 14. ( ) 15.9 (± 10.4) NS 13.4 ( ) 27.0 (± 64.6) 10.9 ( ) 14.9 (± 12.8) NS UFD-1 (µg/l) Median (range) Mean (± SD) 71. ( ) 11.2 (± 8.1) 12.6 ( ) (± 10.21) NS 81.2 ( ) (± 291.2) 84.5 ( ) (± 87.9) NS Turck N. et al., 2009 Intensive Care Medicine, in press.
31 neurological score and 3 biomarkers as individual predictors Specificity (%) Sensitivity (%) WFNS Test set Training set Sensitivity (%) H-FABP Specificity (%) Specificity (%) Partial AUC % Threshold SE (%) SP (%) Partial AUC % Threshold SE (%) SP (%) Training set 3.0 ( ) ( ) 94.1 ( ) Training set 5.1 ( ) ( ) 100 ( ) Test set 3.4 ( ) ( ) 79.2 ( ) Test set 1.9 ( ) ( ) 91.7 ( ) Sensitivity (%) S100! Sensitivity (%) Troponin-I Specificity (%) Specificity (%) Partial AUC % Threshold SE (%) SP (%) Partial AUC % Threshold SE (%) SP (%) Training set 2.0 ( ) ( ) 94.1 ( ) Training set 0.9 ( ) ( ) 94.1 ( ) Test set 3.4 ( ) ( ) 95.8 ( ) Test set 2.6 ( ) ( ) 93.1 ( ) Turck N. et al., 2009 Intensive Care Medicine, in press.
32 neurological score and 3 biomarkers as individual predictors Specificity (%) Sensitivity (%) WFNS Test set Training set Sensitivity (%) H-FABP Specificity (%) Specificity (%) Partial AUC % Threshold SE (%) SP (%) Partial AUC % Threshold SE (%) SP (%) Training Individual set 3.0 performances Training of setthese 5.1 markers not 100 ( ) ( ) ( ) ( ) ( ) ( ) Test set Test set ( ) ( ) ( ) ( ) ( ) ( ) sufficient for a clinical use Troponin-I S100! Sensitivity (%) Sensitivity (%) Specificity (%) Specificity (%) Partial AUC % Threshold SE (%) SP (%) Partial AUC % Threshold SE (%) SP (%) Training set 2.0 ( ) ( ) 94.1 ( ) Training set 0.9 ( ) ( ) 94.1 ( ) Test set 3.4 ( ) ( ) 95.8 ( ) Test set 2.6 ( ) ( ) 93.1 ( ) Turck N. et al., 2009 Intensive Care Medicine, in press.
33 Talk Outlines I. Proteomics strategies for the discovery of brain damage markers II. Diagnosis of Ischemic stroke patients III. Prognosis of Subarachnoid hemorhage patients IV. From single analytes to panels
34 Does combination of parameters improves prediction? Goal: Select from the 18 individual parameters the best panel to improve outcome prediction following aneurysmal subarachnoid hemorrhage How: Iterative permutation-response calculations where each cut-off value was changed iteratively by quintile of 2% increment. Sensitivity and specificity were determined after each iteration until a maximum of sensitivity was achieved for 100% specificity. 1.8x combinations tested Turck N. et al., 2009 Intensive Care Medicine, in press.
35 Sensitivity (%) The best predictor panel 1 clinical scale associated with 5 biomarkers : Troponin I NDKA UFD Panel Training set Test set Partial AUC % 7.8 ( ) 7.3 ( ) Threshold > 2 > 2 SE (%) 77.8 ( ) 70 ( ) SP (%) 100 ( ) 100 ( ) Allows to improve SE of prognosis up to 70%: Rule in 7 out of 10 patients with poor outcome Panel Specificity (%) Specificity (%) Test set Training set Turck N. et al., 2009 Intensive Care Medicine, in press.
36 The best predictor panel AUC (95%CI) WFNS ( ) H-FABP ( ) S ( ) Troponin I ( ) NDKA ( ) UFD ( ) Panel ( ) p Threshold SE (%) < ( ) < !g/L 43 ( ) < !g/L 35 ( ) !g/L 30 ( ) !g/L 18 ( ) !g/L 3 ( ) < * 70 ( ) SP (%) 94 ( ) 92 ( ) 96 ( ) 93 ( ) 93 ( ) 90 ( ) 100 ( )
37 The best predictor panel X AUC (95%CI) WFNS ( ) H-FABP ( ) S ( ) Troponin I ( ) NDKA ( ) UFD ( ) Panel ( ) p Threshold SE (%) < ( ) < !g/L 43 ( ) < !g/L 35 ( ) !g/L 30 ( ) !g/L 18 ( ) !g/L 3 ( ) < * 70 ( ) SP (%) 94 ( ) 92 ( ) 96 ( ) 93 ( ) 93 ( ) 90 ( ) 100 ( )
38 Concluding remarks 1 We demonstrated that: The Tandem Mass Tags is a robust strategy to quantified peptides by mass spectrometry. The post-mortem CSF and brain interstitial fluid samples are powerful models for the discovery of brain damage markers. NDKA and RNA-BP are very early specific diagnostic markers of ischemic stroke (<3 hours).
39 Concluding remarks 2 We demonstrated that WFNS, H-FABP, S100β and Troponin I used individually have interesting prediction power to detect asah with poor outcome. Unfortunately, these are not sufficient for their routine use in clinical practice. In fact, their real impact resides in their combination with NDKA and UFD-1 as a panel. It can rule in specifically 7 out of 10 patients with unfavourable outcome for further management.
40 Concluding remarks 3 Likelihood of success in biomarker discovery is high if: The experiments are design properly at each phase The right samples for discovery are chosen Interdisciplinary teams are put together The validation phase costs are decreased We let time to the markers to find their market niche
41 Acknowledgements Biomedical Proteomics Group, CMU Nadia Walter Maria Ramirez-Boo Yannick Brunner Alexandre Hainard Natacha Turck Domitille Schvartz Feliciano Priego Capote Xavier Robin Natalia Tiberti Loic Dayon Catherine Fouda Alex Scherl Natalia Tiberti Jean-Charles Sanchez NEUCLID, HUG Pierre Burkhard Ghislène Wenger Melanie Cote Neftali Rodrigez Clinical Proteomics Group, HUG Isabelle Demalte Pierre Lescuyer Isabelle Wehrli Véronique Converset Annarita Farina Jacques Deshusses Catherine Zimmermann Denis Hochstrasser Neuroscience, CMU Laszlo Vutskit Vall d Hebron Hospital, Barcelona, Spain. Joan Montaner Anna Rosell Hôpital Pitié-Salpêtrière, Paris Louis Puybasset Paola Sanchez Geneva University & Geneva Hospital Proteome Science plc Swiss National Science Foundation FIND
42 Every Minute Matters Time is Brain
43 Isobaric labeling by TANDEM MASS TAGS N-terminus + Lysine Reporter Balancer Reactive group MS/MS Identification Tandem mass spectrum Quantification
44 Isobaric labeling with OFFGEL electrophoresis and RP-LC Reprinted from ph 1 = pi 1 Peptide 1 ph 2 = pi 2 Peptide 2 Reproducibility ph linearity Orthogonality Number of idendifica:ons Replicate 1 ph pi a b pi Replicate 2 OGE frac)on number t R
45 Stroke diagnosis At the admission: Physician evaluation Sudden confusion, Sudden trouble seeing Sudden weakness or numbness To develop new clinical in one or both eyes Sudden, severe tools headache based on blood trouble speaking of the face (but also arm or leg) or understanding Exclusion of stroke mimics?? (tumor, seizure, hypoglycemia, ) Suspicion of stroke biomarkers to help physicians : Brain Imaging Ischemic stroke? Early diagnosis not Always possible Preventive anti-thrombotic treatment CT-Confirmed Haemorrhagic stroke (high Sensitivity) To rule-in in Hospital ischemic stroke patients (<3 hours) To rule-out out of Hospital mimics-stroke patients To provide tools for prognosis and therapeutic follow-up >24 hrs : MRI 3 days: scanner
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