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TEDMED 2013 Talk


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TEDMED 2013 Talk
Washington, DC

Published in: Health & Medicine, Technology
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TEDMED 2013 Talk

  1. 1. An MRI Showed My Sigmoid Colon WallWas Thickened and Inflamed
  2. 2. I Got a Copyof My MRI Data &Used Calit2 Softwareto Enable Meto Fly ThroughMy Internal Organs
  3. 3. I Searched for Clues AmongMy 150 Blood and Stool Variables, Each Graphed Over 5-10 YearsCalit2 64 megapixel VROOM
  4. 4. Only One Variable Was Far Out of Norm-Complex Reactive Protein From Blood SampleNormal Range<1 mg/LNormal27x Upper LimitCRP Indicates Chronic Episodic Inflammation
  5. 5. By Looking at Stool Samples Over TimeI Discovered My Lactoferrin Was Very Far Above NormalNormal Range<7.3 µg/mL124x Upper LimitLactoferrin Is an Indicator of White Blood Cells Attacking Your Colon
  6. 6. High Lactoferrin Biomarker Values Led Me to HypothesizeI Had Inflammatory Bowel Disease (IBD)My Values 2009-10My Values May 2011Scand J Gastroenterol.42, 1440-4 (2007)IBD is an Autoimmune Disease Which Comes in Two Subtypes:Crohn’s Disease and Ulcerative Colitis
  7. 7. Tracking Multiple Immunological Biomarkers Over TimeLets Me Record the Immune System “Dance”Source: Calit2 Future Health Expedition TeamSignSymptomGut Microbiome Samples
  8. 8. Exploring the Dance Inside Your SuperorganismBetween Your Microbiome and Human Immune SystemYour BodyHas10 TimesAs ManyMicrobe CellsAsHuman CellsInclusion of MicrobiomeWill Radically Change Medicine
  9. 9. Computing and Visualizingthe Genomic Dance of the MicrobesSequencing by JCVI or Human Microbiome ProgramRequired 25 CPU-Years on SDSC Gordon SupercomputerCalit2 VROOM-FuturePatient Expedition
  10. 10. Almost All Abundant Species (≥1%) in Healthy SubjectsAre Severely Depleted in LS GutSource: Sequencing JCVI; Analysis Weizhong Li, UCSD; HMP, NIH; UCSD SOMLS December 28, 2011 Stool Sample
  11. 11. Rare Species Take Over the Altered Microbial EcologyIn LS vs. Average Healthy152x765x148x849x483x 220x201x522x169xNumber Above LS Blue Baris Multiple of LS AbundanceCompared toAverage Healthy AbundancePer SpeciesSource: Sequencing JCVI; Analysis Weizhong Li, UCSD, HMP, NIHLS December 28, 2011 Stool Sample
  12. 12. When We Think About Biological DiversityWe Typically Think of the Wide Range of AnimalsBut All These Animals Are in One SubPhylum Vertebrataof the Chordata PhylumAll images from Wikimedia Commons.Photos are public domain or by Trisha Shears & Richard Bartz
  13. 13. Think of These Phyla of AnimalsWhen You Consider the Biodiversity of Microbes Inside YouAll images from WikiMedia Commons.Photos are public domain or by Dan Hershman, Michael Linnenbach, Manuae, B_coolPhylumAnnelidaPhylumEchinodermataPhylumCnidariaPhylumMolluscaPhylumArthropodaPhylumChordata
  14. 14. We Found Major Shifts in Microbial Ecology PhylaBetween Healthy and Two Forms of IBDCollapse ofBacteroidetesExplosion ofProteobacteriaMostCommonMicrobialPhylaMicrobiome “Dysbiosis”or “Mass Extinction”?
  15. 15. I Can Track Changes in My Microbiome Before and After1 Month Antibiotic & 2 Month Prednisone TherapyTherapy Greatly Reduced Two Phyla,But Massive Reduction in BacteroidetesAnd Large % Proteobacteria RemainReduced 45xReduced 90xSmall ChangesWith No TherapyI am Trapped in a Local Ecological Equilibrium“Far from Home”
  16. 16. Refining the Dance• I Now Know Where I Am• And Where I Need to Get to• Startups Enable Tracking the Dance• Novel Interventions Become PossibleWhere There is DataThere is Hope