the human plasma proteome

Transcription

1 Developmental proteomics: the importance of age specific differences in the human plasma proteome A/Prof Vera Ignjatovic Haematology Research Laboratory, MCRI RCPA Introduction to Proteomics in Pathology 2 nd November 2017 Sydney, Australia

2 Melbourne Children s Campus 4000 staff Murdoch Children s Research Institute Custodian of research on campus Recognized globally for its child health discoveries University of Melbourne Custodian of education on campus The best University in Australia (32 nd worldwide) Royal Children s Hospital Major specialist paediatric hospital in Australia State-wide major trauma center for Paediatrics Nationally Focused Centre for cardiac and liver transplantation 2

3 Royal Children s Hospital in numbers 45,474 inpatients 88,654 Emergency presentations 225,150 Outpatient appointments 460 Children receive community care 13,187 Children undergo surgery 3

4 Haematology Research Team Developmental Haemostasis Age-related differences in the blood clotting system. Differences in: Concentration, Function and Structure of haemostatic proteins Response to Anticoagulants (Heparin, LMWH, Rivaroxaban, Dabigatran) Platelet phenotype and response to agonists Mechanism of Thrombin generation Clot structure and response to fibrinolysis Understanding age-specific normative changes are the key in our ability to provide prevention strategies and evidence based treatment and to improve clinical outcomes for children. 4

5 Access to blood samples Healthy Neonates Family Birthing Unit or post natal wards Gestation >37 weeks, Birth-weight >2500gm, APGAR (5min) 7, absence of systemic abnormalities Up to 72 hours post birth Neonates born prematurely (32-36 weeks) but healthy Healthy Children 1 month to 18 years about to undergo minor/elective day surgery No past or family history of major disorders; no medications Proteomics is the perfect approach to utilise these samples to their maximum capacity for advancing the knowledge and improving the health of children. 5

6 Defining Normal To know someone is unwell, we have to know how they deviate from normal To know if someone is getting better, we have to know if we are returning them to normal To know if someone is well, we have to understand normal However you cut it, we have to understand normal The biology of growth and development is fundamental to human survival For too long children have been second class citizens: we have an opportunity to change Courtesy of Prof Paul Monagle 6

7 HAPPI Kids Study Prospective Reference Ranges for: Biochemistry (> 30 analytes) Immunology (>15 analytes) Haematology (>20 analytes) Analyser to analyser comparison Across method comparison 4 sites (RCH, RWH, Northern, Western) 6 laboratories (RCH, RMH, Melbourne Path, Dorevitch, ACL, Monash Path) Healthy prem babies (>32 weeks) to 18 year olds ~3000 samples collected to date 7

8 Reference Ranges for Creatinine Males Females 8

9 Proteomics studies to date Identification of biomarkers Detecting the highest number of proteins Effect of drugs on changes in protein expression Majority focused on adults Very few studies and hence very limited knowledge of the proteome in infants and children. 9

10 Children Healthy children 98.6% 99.4% 4 proteomics studies focusing on healthy children 10

11 What we don t know and why it matters Normal proteomic data absent in children A significant gap in our understanding of what constitutes a normal proteome across different biological mediums. We have minimal knowledge of the changes in protein expression that take place with age in the healthy population. Biomarker efforts near impossible This knowledge is critical for early disease detection and development of prevention strategies that will improve the health of our population across the age spectrum. Understanding age-specific changes in protein expression will place the focus on disease prevention rather than treatment. 11

12 Paediatric Proteomics (PediOme) Human Proteome Organisation (HUPO) initiative Established in late 2013 The vast majority of proteomic studies carried out in adults Absence of Normal proteomic data in children Lack of high quality Pediatric biorepositories and samples 12

13 HUPO Initiatives 13

14 PediOme Aims Characterize normal paediatric proteome Birth to adulthood Detail Coordinate longitudinal studies Optimize storage matrices Standardize the protocols for paediatric proteomic studies Enhance capabilities for translational research World wide biorepositories network and inventory Blood, Blood spots, Saliva, Stool, Urine, etc. Sample collection, storage, standards, etc. Common forum for collaboration between clinicians and scientists. Facilitate studies in the setting of major and unique diseases affecting the pediatric population Infectious Diseases, Autism Spectrum Disorders, Diabetes, Obesity To introduce proteomics as a stream at major paediatric clinical congresses and promote training of clinical staff (clinicians and nursing staff). 14

15 PediOme Progress Proteomics Clinical Applications - Paediatric edition - PediOme session at HUPO Congress - Clinical Proteomics - Thematic series on the PediOme - PediOme session at HUPO Congress 15

16 Developmental Proteomics Age-specific changes in protein expression in the healthy population for any given proteome = Healthy State Physiologically predictable age-specific changes in protein expression as a reference point for early detection of disease (e.g. when protein expression deviates from that expected in the healthy population) Protein expression curves akin to growth charts to monitor the health status of an individual, allowing early detection of variation from that predicted by the population. Early identification of the individuals susceptible to specific diseases (e.g. diabetes) Delivering accurate and targeted clinical outcome 16

17 Developmental Proteomics 17

18 2017;152: Longitudinal data focusing on changes in human plasma proteome during childhood. Plasma proteome in 10 healthy children during their development (9 time points; birth to puberty = 9 months - 14 years of age) Samples: - Diabetes Autoimmunity Study in the Young (DAISY) cohort. - Healthy children negative for islet autoantibodies during follow-up. 18

19 Results and Conclusion (Liu C-W et al.) Age-dependent expression for >50% of proteins Age-matched studies are critical in the paediatric setting Knowledge of the age-specific changes in protein expression during childhood Reference set for proteomic biomarker studies in childhood (9 months 14 years) 19

20 Mol Cell Pro 2017; 16: Aim: To quantitate age-specific variability of plasma proteins in healthy, neonates, children and adults. Venous blood, Citrated tubes; 3000 rpm, 10 min, 10 C; plasma stored at 80 C Age-group N (F/M) Age (median) Age (range) Neonates 5/5 Within 72 hrs post birth < 1 year 3/7 7.7 months 6 11 months 1 5 years 5/5 3.1 years years Adults 5/ years years 20

21 SWATH-MS approach Does not rely on prior knowledge of precursor peptide ions Data Independent Acquisition Can measure the same peptides across all samples Confident identification and quantification of peptides over a dynamic range of 4 orders of magnitude. Useful tool for quantitative analysis of biological specimens such as plasma. Not yet fully exploited for human plasma biomarker discovery. 21

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23 Hierarchical Clustering 107 proteins differentially expressed across age (ANOVA, p < 0.05, fold change > 1.5) 23

24 Top Enriched Pathways (% overlap) Acute phase response signaling (18.1%) LXR/RXR (lipid metabolism, inflammation) Activation (19.5%) FXR/RXR (lipoprotein, lipid and glucose metabolism) Activation (17.4%) Complement system (34.2%) Coagulation system (34.3%) 24

25 Most Significant Networks Hematological System Development/Function Neurological Disease, Lipid Metabolism, Molecular Transport Humoral Immune Response, Inflammatory Response Red = up-regulation in neonates compared to adults; Green = down-regulation in neonates. 25

26 Conclusions and Significance First study to utilize SWATH-MS technology to quantify and analyze variability in differential protein expression in both adult and pediatric agespecific contexts. Plasma proteome changes significantly as the system ages. Proteins involved in hematopoietic development and function, the immune system, and physical growth undergo significant change in expression as the plasma proteome ages. Provides reference ranges for protein expression that can be used as a comparison in the context of health monitoring or disease investigation. 26

27 J Proteomics 2015;123:78-88 Proteome Secretome Children Adults Children Adults Number (M/F) 11 (4/7) 11 (4/7) 8 (5/3) 8 (2/6) Age median (Range) 4.3 ( ) 35.1 ( ) 5.2 ( ) 34.4 ( ) 27

28 Results Platelet Proteome A. Adult Sample (Cy3) B. Paediatric sample (Cy5) C. Overlay ~837 protein spots per gel 28

29 Results Platelet Proteome Protein ID Average Ratio (children : adults) P value Thrombospondin Serotransferrin Fibrinogen alpha chain Serum Albumin Glyceraldehyde-3-phosphate dehydrogenase Transgelin Calponin-2 LIM SH3 domain protein HCG (Possible J 56 gene segment)

30 Results Platelet Releasate Protein ID Average Ratio (children:adults) P value Thrombospondin Gelsolin Factor XIII A chain Factor XIII B chain Gelsolin Serotransferrin Fibrinogen gamma chain Actin, cytoplasmic 1 Beta-actin; Plasminogen activator inhibitor Tropomyosin 3 (TPM3) Tropomyosin Basement-membrane protein Secreted protein acidic and rich in cysteine

31 Canonical Pathways 31

32 Conclusions and Significance Significant differences in the expression of platelet proteins and proteins secreted in response to platelet activation in healthy children compared to healthy adults. Identified proteins play important roles in processes such as platelet aggregation and plaque stabilization. In this context they could be important in: Normal Growth and Development Protective mechanism against disease Potential biomarkers for susceptibility to disease Targets for pharmacological therapies 32

33 Why Paediatric Proteomics and why NOW? Children are epidemiologically & physiologically diverse, but fundamentally different from adults. Necessary for comprehensive/holistic study of disease. Proteomic approaches are developing at an extremely fast pace (decrease in complexity of methods and cost, increase in level of information) Focus on translation of proteomics methods to the clinical setting Paediatric biomarker studies are significantly simplified as children tend to suffer from one condition at a time, in contrast to adults where confounding co-morbidities are often present. 33

34 Developmental Proteomics in Practice Developmental proteomics is the key in providing the knowledge needed to detect and prevent disease in humans and to improve human health. Obtaining funding and completing such studies represents a difficult scenario. Obstacles can be overcome with a concerted, international effort to define the age-specific changes in protein expression across different proteomes. PediOme initiative is an ideal avenue for collaboration needed to place developmental proteomics on the agenda and to make these studies happen. If you interested in being involved: Vera.ignjatovic@mcri.edu.au 34

35 Acknowledgments Royal Haematology Children s Research, MCRI Hospital, Australian Melbourne Proteome Analysis Facility Paul Monagle Vasiliki Karlaftis Chantal Attard Stefan Bjelosevic Christina Yip Charmaine Cini Healthy Children Mark Molloy Dana Pascovici Anesthetic and Surgical Departments Thiri Zaw Xiaomin Song Royal Women s Hospital, Jemma Melbourne Wu Healthy Adult Volunteers Healthy Newborns Post-natal ward 35

36 Thank you