DETECTING DISEASE IN BLOOD

Transcription

1 Science Webinar Series DETECTING DISEASE IN BLOOD What mirna Biomarkers Can Tell Us 30 May, 2012 Change the size of any window by dragging the lower left corner. Use controls in top right corner to close or maximize each window. What each widget does: shows the audio media player opens the Ask a Question box download slides and more info shows slide window shows speaker bios search Wikipedia Facebook login Twitter login (#ScienceWebinar) LinkedIn login if you need help

2 Science Webinar Series DETECTING DISEASE IN BLOOD What mirna Biomarkers Can Tell Us 30 May, 2012 Brought to you by the Science/AAAS Custom Publishing Office Participating Experts: Colin C. Pritchard M.D., Ph.D. University of Washington Seattle, WA Monty Montano, Ph.D. Boston University School of Medicine Boston, MA Adam Baker, Ph.D. Exiqon Vedbaek, Denmark Sponsored by:

3 Circulating microrna as Disease Biomarkers: A Laboratory Medicine Perspective Colin C. Pritchard MD, PhD University of Washington Department of Laboratory Medicine Science Webinar, May 30, 2012

4 Outline microrna as circulating biomarkers Laboratory medicine considerations: Sources of variation State of microrna in plasma Origin i and implications for disease specificity it

5 Circulating microrna Are Attractive Biomarkers Abundant in Blood Easy to Measure Highly Stable Disease Associations

6 Over 200 Publications Since 2008 on Circulating mirna Cancer Prostate, Breast, Colon, Lung, Ovarian, Leukemia Many other diseases Pregnancy, Diabetes, Heart Disease, etc. Sources of variation not well-studied

7 Outline microrna as circulating biomarkers Laboratory medicine considerations: Sources of variation State of microrna in plasma Origin i and implications for disease specificity it

8 Sources of Variation Analytical Biological

9 Analytic Variation Pre-analytic Analytic Post-analytic

10 Interferences Hemolysis Lipemia Drugs Antibodies Hemolysis Lipemia

11 Biological Variation Within individual Between individual Diurnal Age/Gender Fasting/Fed Genetic/Ethnicity Sick/Well Chronic disease

12 Outline microrna as circulating biomarkers Laboratory medicine considerations: Sources of variation State of microrna in plasma Origin i and implications for disease specificity it

13 How is mirna Stable in Plasma? RNase-resistance hypotheses: Intrinsically stable? (no) Protected in vesicles? (one model) Protected by other mechanisms?

14 Two Populations of Circulating mirna detected by size-exclusion chromatography Vesicle/Exosome Protein Complex Relative e Copies mir-142-3p Relative e Copies mir Vesicle Protein Relative Size Vesicle Protein Relative Size Adapted from Arroyo et al. (2011) PNAS

15 Implications of Two Plasma States For Circulating mirna Biomarkers?

16 Specimen Processing and Vesicles Numbe er Per ml 2x10 6 2x10 6 Vesicles Vesicles Platelets Platelets Plasma Platelet-Poor Plasma Particle 3x10 5 Vesicles Platelets Platelet-Poor Plasma Filtered Diameter (µm)

17 Outline microrna as circulating biomarkers Laboratory medicine considerations: Sources of variation State of microrna in plasma Oi Origin i and dimplications for disease specificity it

18 Where do plasma mirna come from? Cell Origin i Relative Contribution ti Blood Cells?? Endothelium?? Other Tissues??

19 Plasma and Blood Cell mirna Levels are Correlated Plasma Blood Cells RBC myeloid lymph higher 79 mirna Biomarkers mirna level lower Healthy Donors Adapted from Pritchard et al. (2012) Cancer Prev. Res.

20 Plasma mirna Correlate To Blood Counts mir-223 mir log 10 copies s/µl plasma 8.0 R= log 10 copies s/µl plasma 6.5 R= Neutrophil Count (log 10 thou/µl) Lymphocyte Count (log 10 thou/µl) Consecutive Clinical Plasma Samples Adapted from Pritchard et al. (2012) Cancer Prev. Res.

21 RBC-Derived mirna are Affected by Hemolysis mir-16, mir-451 increased up to 50-fold Non-RBC mirna not impacted e.g. mir-122, mir-223, mir-150 McDonald et al. (2011) Clin. Chem. Pritchard et al. (2012) Cancer Prev. Res.

22 Summary/Conclusions Circulating mirna are promising as disease biomarkers Little is known about analytic properties or biologic variation mirna are present in at least two states in plasma Plasma mirna are likely released by blood cells Plasma mirnas that are abundant in normal blood cells may have poor specificity as biomarkers because they are influenced by cell counts and hemolysis

23 Acknowledgements FHCRC Evan Kroh Muneesh Tewari Jason Arroyo Brent Wood Heather Cheng Liz Setran Hye Son Yi John Tait UH Don Gibson Marc Goodman Deb Barden Yeonju Kim UW

24 Science Webinar Series DETECTING DISEASE IN BLOOD What mirna Biomarkers Can Tell Us 30 May, 2012 Brought to you by the Science/AAAS Custom Publishing Office Participating Experts: Colin C. Pritchard M.D., Ph.D. University of Washington Seattle, WA Monty Montano, Ph.D. Boston University School of Medicine Boston, MA Adam Baker, Ph.D. Exiqon Vedbaek, Denmark Sponsored by:

25 AGING AND CHRONIC DISEASE: microrna PROFILING in CENTENARIANS and HIV INFECTION MONTY MONTANO, PhD Principal Investigator Section of Infectious Diseases, Boston University School of Medicine Boston OAIC Pepper Center for Aging New England Centenarian Study

26 QUESTIONS POSED IN THIS PRESENTATION I. Is there evidence for micrornas in aging?

27 QUESTIONS POSED IN THIS PRESENTATION I. Is there evidence for micrornas in aging? II. Can blood microrna profiling be used to study aging in the extreme?

28 QUESTIONS POSED IN THIS PRESENTATION I. Is there evidence for micrornas in aging? II. Can blood microrna profiling be used to study aging in the extreme? Centenarians

29 QUESTIONS POSED IN THIS PRESENTATION I. Is there evidence for micrornas in aging? II. Can blood microrna profiling be used to study aging in the extreme? III. Can blood microrna profiling be used to study chronic infection?

30 QUESTIONS POSED IN THIS PRESENTATION I. Is there evidence for micrornas in aging? II. Can blood microrna profiling be used to study aging in the extreme? III. Can blood microrna profiling be used to study chronic infection? HIV infection

31 QUESTIONS POSED IN THIS PRESENTATION I. Is there evidence for micrornas in aging? II. Can blood microrna profiling be used to study aging in the extreme? III. Can blood microrna profiling be used to study chronic infection? IV. Summary and implications for future studies

32 QUESTIONS POSED IN THIS PRESENTATION I. Is there evidence for micrornas in aging?

33 THE AGING BRAIN BASED ON microrna EXPRESSION AGE Adapted from Montano et al, Aging Res Rev 2010

34 QUESTIONS POSED IN THIS PRESENTATION I. Is there evidence for micrornas in aging? II. Can blood microrna profiling be used to study aging in the extreme?

35 microrna PROCESSING AS A BIOMARKER OPPORTUNITY pri-microrna

36 microrna PROCESSING AS A BIOMARKER OPPORTUNITY pri-microrna Biomarkers in Plasma/Serum?

37 CORRELATED microrna EXPRESSION IN CENTENARIAN SAMPLES CENT-1 CENT-2

38 COMPARATIVE MICRORNA PROFILING OF CENTENARIANS Cq level microrna Exiqon average Centenarians

39 COMPARATIVE MICRORNA PROFILING OF CENTENARIANS above average Cq level microrna Exiqon average Centenarians

40 MICRORNA PROFILING OF CENTENARIANS by GENDER

41 MICRORNA PROFILING OF CENTENARIANS by GENDER below average

42 QUESTIONS POSED IN THIS PRESENTATION I. Is there evidence for micrornas in aging? II. Can blood microrna profiling be used to study aging in the extreme? III. Can blood microrna profiling be used to study chronic infection?

43 HIV INFECTION AND PHENOCOPIES OF AGING Frailty related phenotype Desquilbet et al., 2007; Effros et al., 2008; Fried et al., 2001 Decline in bone and muscle mass Brown et al., 2009; Brown and Qaqish, 2006, Banerjee et al., 2012 Systemic inflammatory burden Finch and Morgan, 2007; Yarasheski et al., 2005 Immuosenescence elevated Effros 2008, Appay 2007 Cognitive and brain function decline Ances et al., 2009

44 COMPARATIVE MICRORNA PROFILING OF SIV INFECTION SIV+ SIV- SIV+ SIV-

45 COMPARATIVE MICRORNA PROFILING OF SIV INFECTION SIV+ SIV- SIV+ SIV-

46 CLUSTERING BASED ON MICRORNAS AND SAMPLES Serum samples Serum samples micr rornas mic rornas SIV SIV+ SIV SIV+ Rescaled by row (micrornas) Rescaled by columns (samples)

47 CLUSTERING SERUM AND HIPPOCAMPUS microrna EXPRESSION Serum samples Brain samples mic crornas mi crornas

48 CLUSTERING SERUM AND HIPPOCAMPUS microrna EXPRESSION Serum samples Brain samples mic crornas mi crornas

49 QUESTIONS POSED IN THIS PRESENTATION I. Is there evidence for micrornas in aging? II. Can blood microrna profiling be used to study aging in the extreme? III. Can blood microrna profiling be used to study chronic infection? IV. Summary and implications for future studies

50 SUMMARY and IMPLICATIONS micrornas may reflect underlying tissue/organ processes

51 SUMMARY and IMPLICATIONS micrornas may reflect underlying tissue/organ processes microrna signatures may distinguish biologic from chronologic age

52 SUMMARY and IMPLICATIONS micrornas may reflect underlying tissue/organ processes microrna signatures may distinguish biologic from chronologic age micrornas may be useful biomarkers for acute and chronic infection

53 SUMMARY and IMPLICATIONS micrornas may reflect underlying tissue/organ processes microrna signatures may distinguish biologic from chronologic age micrornas may be useful biomarkers for acute and chronic infection micrornas may be useful in targeted t therapeutic-diagnosticsti ti

54 ACKNOWLEDGEMENTS AGING STUDIES Paola Sebastiani Tom Perls Kim Kafadar Long Clinton Baldwin Greg Gibson Adam Baker HIV STUDIES Daniel Michaels Susan Westmoreland NECS, Boston University NECS, Boston University Boston University Boston University Georgia Institute of Technology Exiqon, Inc. Boston University NEPRC, Harvard University SUPPORT NIA NIAMS NIAID

55 Science Webinar Series DETECTING DISEASE IN BLOOD What mirna Biomarkers Can Tell Us 30 May, 2012 Brought to you by the Science/AAAS Custom Publishing Office Participating Experts: Colin C. Pritchard M.D., Ph.D. University of Washington Seattle, WA Monty Montano, Ph.D. Boston University School of Medicine Boston, MA Adam Baker, Ph.D. Exiqon Vedbaek, Denmark Sponsored by:

56 Science Webinar May 30 th 2012, Adam Baker, PhD. Translating mirna discovery in biofluids into robust biomarkers for disease, toxicology or injury studies

57 Agenda How to study micrornas introduction to LNA Detection of micrornas in clinical samples Diagnostic development using LNA Universal RT microrna PCR Toxicology new focused platform and services

58 Analyzing micrornas overcoming challenges by using LNA Feature Challenge LNA allows Short sequences (19-22 nt) Hard to achieve high sensitivity Increased affinity Highly homologous families (single base differences) Hard to achieve sufficient specificity Single nucleotide discrimination Large variation in base composition (GC content varies between 5-95%) Hard to design good multiplex assays Tm normalization

59 LNA enables high sensitivity and high specificity in hybridization assays Increased Tm (Tm increases by 2-8ºC per base) Increased Tm (larger difference between mismatch and perfect match) Tm normalization (adjust oligos to the same Tm) K. Bondensgaard et al., Chem. Eur. J. 2000, 6, 2687 M. Petersen et al., J. Am. Chem. Soc. 2002, 124, 5974

60 Searching for microrna biomarkers is like looking for a needle in a Haystack. A cell contains Approximately 10 to 30pg of total RNA total RNA level in plasma is in the range ng/ml. 0.3% of this is microrna 5% of this microrna Persat, Alexandre; Chivukula, Raghu R.; Mendell, Joshua T.;Santiago, Juan G. Jensen et al. BMC Genomics 2011, 12:435 Journal Title: Analytical Chemistry - Columbus 60 ISSN:

61 LNA microrna PCR System: ideal for finding needles Advantages: Universal RT no bias, no pre-amplification (no extra hay generated) LNA in two specific primers sensitivity and specificity (teases out the needle from the hay)

62 Extreme sensitivity allows microrna PCR profiling Extreme sensitivity allows microrna PCR profiling from clinical samples

63 Accurate microrna PCR profiling with simple workflow 20 µl plasma/serum or 150pg RNA input/ One RT reaction 96 or 384-well PCR including calibrators / controls QC / normalization and data analysis

64 mircury LNA microrna PCR System mircury LNA microrna PCR System - a solution for every project

65 Agenda How to study micrornas introduction to LNA Detection of micrornas in clinical samples Diagnostic development using LNA Universal RT microrna PCR Toxicology new focused platform and services

66 LNA PCR assays show linearity at very low concentrations as found in plasma and serum Plasma or serum Serial dilution of a pool of 647 synthetic ti micrornas Correlation between microrna input and median Ct LNA PCR assays show near perfect linearity even at very low concentrations

67 We are experienced at overcoming the challenges of microrna qpcr normalization in serum/plasma Normalization adjusts for technical biases (RNA amount, quality etc) No housekeeping genes are stably expressed in all situations U6 and 5S are not applicable to serum/plasma samples With qpcr panels, no prior assumptions about housekeeping genes Select a normalization method appropriate for the dataset Raw data values Mean centered (top 50 expressed) normalization Mean centered normalization Quantile normalization

68 Unique QC possibilities with our Normal reference range Human serum human samples with over 1 million PCR data points make up the reference range Dynamic Window Of mirna Expression In serum

69 Agenda How to study micrornas introduction to LNA Detection of micrornas in clinical samples Diagnostic development using LNA Universal RT microrna PCR Toxicology new focused platform and services

70 Early Detection of CRC in blood plasma addresses large unmet need Colorectal cancer The second most important cancer in terms of deaths in the western world Estimated deaths in 2009 in the USA was 49,920 The addressable screening market is 3.75 Billion USD (or 300 million people per year) Stage 5 yr relative Treatment survival 0-I 93% Surgery II 80% Surgery III 58% Surgery/adjuvant chemotherapy IV 6.9% Chemotherapy

71 Exiqon s discovery process and PCR platform Exiqon s discovery process and PCR platform are compatible with clinical procedures

72 Development of microrna Early Detection Test of CRC in blood plasma DISCOVERY PHASE VALIDATION PHASE Genome wide screening Normalization, QC, processing Candidate mirna discovery screen Bioinformatics, data analysis Validation Set mirna signature 50 controls 50 CRC patients 742 mirna screen Genome wide Multiple QC check Data flagging Normalization 325 samples Focused Serum/Plasma panel Multiple controls Data analysis Quality control ROC curve mirna selection Defined mirna signature Pick & Mix panel Multiple controls

73 microrna Biomarker discovery workflow and panel selection options DISCOVERY PHASE VALIDATION PHASE Genome wide screening Normalization, QC, processing Candidate mirna discovery screen Bioinformatics, data analysis Validation Set mirna signature

74 Agenda How to study micrornas introduction to LNA Detection of micrornas in clinical samples Diagnostic development using LNA Universal RT microrna PCR Toxicology new focused platform and services

75 Focus microrna PCR Panels Available from the Pick & Mix configurator allows for full customization to improve sample analysis Focus panels are available for customization through the Pick&Mix configurator:

76 New Focused PCR development

77 Acknowledgements

78 Science Webinar Series DETECTING DISEASE IN BLOOD What mirna Biomarkers Can Tell Us 30 May, 2012 Brought to you by the Science/AAAS Custom Publishing Office Participating Experts: Colin C. Pritchard M.D., Ph.D. University of Washington Seattle, WA Monty Montano, Ph.D. Boston University School of Medicine Boston, MA Adam Baker, Ph.D. Exiqon Vedbaek, Denmark To submit your questions, type them into the text box and click. Sponsored by:

79 Science Webinar Series DETECTING DISEASE IN BLOOD What mirna Biomarkers Can Tell Us 30 May, 2012 Brought to you by the Science/AAAS Custom Publishing Office Look out for more webinars in the series at: To provide feedback on this webinar, please e mail your comments to webinar@aaas.org For related information on this webinar topic, go to: Sponsored by: