janssen immune system_&_microbiome_022213 (1)

“Dynamics of the Interaction Between the Human Gut Microbiome and Immune System”

Discussion

Janssen La Jolla Research and Development

La Jolla, CA

February 22, 2013

Dr. Larry Smarr

Director, California Institute for Telecommunications and Information Technology

Harry E. Gruber Professor,

Dept. of Computer Science and Engineering

Jacobs School of Engineering, UCSD

http://lsmarr.calit2.net

1

From Measuring Macro-Variables to Measuring Your Internal Variables

www.technologyreview.com/biomedicine/39636

From One to a Billion Data Points Defining Me:The Exponential Rise in Body Data in Just One Decade!

Billion: My Full DNA,MRI/CT Images

Million: My DNA SNPs,Zeo, FitBit

Hundred: My Blood VariablesOne: My WeightWeight

BloodVariables

SNPs

Microbial Genome

Improving Body

Discovering Disease

Visualizing Time Series of 150 LS Blood and Stool Variables, Each Over 5 Years

Calit2 64 megapixel VROOM

Complex Reactive ProteinFrom Blood Sample

Normal Range<1 mg/L

Normal

27x Upper Limit

Antibiotics

Antibiotics

Peak Sec IgA, Lysozyme 1/30/12Peak CRP, Calprotectin 12/28/11Peak Lactoferrin 5/2/11

Lactoferrin From Stool Sample

Normal Range<7.3 µg/mL

124x Upper Limit

Antibiotics


Antibiotics

High Lactoferrin Biomarker Led Me to Hypothesis I Had Inflammatory Bowel Disease (IBD)

IBD is an Autoimmune Disease Which Comes in Two Subtypes: Crohn’s and Ulcerative Colitis

High Level of Calprotectin Confirmed Hypothesis

Scand J Gastroenterol. 42, 1440-4 (2007)

My Values 2009-10

My Values May 2011

Colonoscopy Images Show Sigmoid Colon Inflammation

Dec 2010

May 2011

Descending Colon

Sigmoid ColonThreading Iliac Arteries

Major Kink

Confirming the IBD (Crohn’s) Hypothesis:Finding the “Smoking Gun” with MRI Imaging

I Obtained the MRI Slices From UCSD Medical Services

and Converted to Interactive 3D Working With

Calit2 Staff & DeskVOX Software

Transverse ColonLiver

Small Intestine

Diseased Sigmoid ColonCross Section

MRI Jan 2012

Comparison of DeskVOX with Clinical MRI Slice Program

Interactively Exploring My BodyWith Calit2 Virtual Reality Facilities

Photo & CalVR software Courtesy of Jurgen Schulze, Calit2

StarCAVE

www.youtube.com/watch?v=9c4DtJ_L_Ps

zSpace

TourCAVE

VROOM

Connecting Colonoscopy “Inside View”With MRI “Outside View”

LS Colon Images and Colonoscopy VideoOn Calit2 Director’s Colony OptIPortable Wall

Why Did I Have an Autoimmune Disease like IBD?

Despite decades of research, the etiology of Crohn's disease

remains unknown. Its pathogenesis may involve a complex interplay between

host genetics, immune dysfunction,

and microbial or environmental factors.--The Role of Microbes in Crohn's Disease

Paul B. Eckburg & David A. RelmanClin Infect Dis. 44:256-262 (2007)

So I Set Out to Quantify All Three!

I Wondered if Crohn’s is an Autoimmune Disease, Did I Have a Personal Genomic Polymorphism?

From www.23andme.com

SNPs Associated with CD

Polymorphism in Interleukin-23 Receptor Gene

— 80% Higher Risk of Pro-inflammatoryImmune Response

NOD2

ATG16L1

IRGM

Now Comparing 163 Known IBD SNPs

with 23andme SNP Chip

Crohn’s May be a Related Set of Diseases Driven by Different SNPs

Me-MaleCD Onset

At 60-Years Old

Female CD Onset

At 20-Years Old

NOD2 (1)rs2066844

Il-23Rrs1004819

White Blood Cell CountFrom Blood Sample

Normal Range4-10,000 cells/µL

AntibioticsNormal


Neutrophils as % of WBCsFrom Blood Sample

Normal

Normal Range31-71%


Lymphocytes as % of WBCsFrom Blood Sample

Normal

Antibiotics


Lymphocytes Include B Cells, T cells, and Natural Killer Cells

Eosinophils as % of WBCsFrom Blood

Normal

Normal Range1-7%


Antibiotics

Monocytes as % of WBCsFrom Blood

Normal Range5-12%


Normal

CalprotectinFrom Stool Sample

Normal Range<50 µg/g

50x Upper Limit

Antibiotics


Secretory IgAFrom Stool Sample

Normal Range54-204 mg/dL

Normal

7x Upper LimitPeak Sec IgA, Lysozyme 1/30/12Peak CRP, Calprotectin 12/28/11Peak Lactoferrin 5/2/11

Antibiotics

Antibiotics

Lysozyme From Stool Sample

Normal Range<600 ng/mL

Normal

2x Upper Limit

AntibioticsPeak Sec IgA, Lysozyme 1/30/12Peak CRP, Calprotectin 12/28/11Peak Lactoferrin 5/2/11

Antibiotics

Putting Multiple Immunological Biomarker Time Series Together, Reveals Major Immune Dysfunction

Green : Inside RangeOrange: 1-10x OverRed: 10-100x OverPurple: >100x Over

Source: Calit2 Future Health Expedition Team

Four Immune Biomarkers Over TimeCompared with Four Signs/Symptoms

Here Immune biomarkers are normalized 0 to 1, with 1 being the highest value in five years

Source: Photo of Calit2 64-megapixel VROOM

Microbes are 90% of Your Cells-So I Set Out to Determine My Gut Microbes & Their Time Variation

Shipped Stool SampleDecember 28, 2011

I Receiveda Disk Drive April 3, 2012With 35 GB FASTQ Files

Weizhong Li, UCSDNGS Pipeline:230M Reads

Only 0.2% Human

Required 1/2 cpu-yr at SDSCPer Person Analyzed!

First Surprise:Almost All My DNA Abundances are Viral!

LS Viral Species Comprise >97% Relative Abundance of Virus + Bacteria + Archaea

LS Virus Species Which Are >1% of Total Abundance

In an Average Healthy Person,None of LS Viruses Exceed 0.01% of the Total Relative Abundance of Viruses + Bacteria

In Average Healthy Person, Viruses Are <2% of Total Abundance

My Viral Load is Mainly SP-6 Like

What is a “Healthy” Gut Microbiome?Considerable Phyla Variation Found in HMP

Source: “Structure, function and diversity of the healthy human microbiome,” HMP Consortium, Nature, 486, 207-212 (2012)

Note: Euryarchaeota Are So RareThat They Arent Graphed!

Phyla Gut Microbial Abundance Without Viruses: LS, Crohn’s, UC, and Healthy Subjects

Crohn’s UlcerativeColitis

HealthyLS

Toward Noninvasive Microbial Ecology Diagnostics

Source: Weizhong Li, UCSD; Calit2 FuturePatient Expedition

LS Time Series Gut Microbiome Classesvs. Healthy, Crohn’s, Ulcerative Colitis

Microbial Metagenomics Can Diagnose Disease States Using Principal Component Analysis

From www.23andme.com

SNPs Associated with CD

Mutation in Interleukin-23 Receptor Gene—80% Higher

Risk of Pro-inflammatoryImmune Response

2009

IBD Patients Harbored, on Average, 25% Fewer

Microbial Genes than the Individuals

Not Suffering from IBD.

Principal Component AnalysisOn Microbial Species Abundance

Healthy, CD, UC and LSRelative Abundance of Proteobacteria to Actinobacteria

Bacteroides fragilis Levels Different ForHealthy and IBD Human Gut-Differentiates CD and UC

HealthyUlcerative

Colitis

Crohn’sDisease

LS

Source: Analysis by LS working on Weizhong Li Data

Almost All Abundant Species (≥1%) in Healthy SubjectsAre Severely Depleted in LS Gut

Top 20 Most Abundant Microbial SpeciesIn LS vs. Average Healthy Subject

152x

765x

148x

849x483x

220x201x

522x169x

Number Above LS Blue Bar is Multiple

of LS Abundance Compared to Average Healthy Abundance

Per Species

Source: Sequencing JCVI; Analysis Weizhong Li, UCSDLS December 28, 2011 Stool Sample

Comparing 3 LS Time Snapshots (Left) with Healthy, Crohn’s, UC (Right Top to Bottom)

Calit2 VROOM-FuturePatient Expedition

LS Gut Microbe Species 12/28/11 (red)compared to Average of 35 Healthy Subjects (blue)

Derived from metagenomic sequencing of LS stool sample.Each species is a bar,

height is logarithmic abundance, species are divided into microbial phyla


200 LS Gut Microbe Species at 3 Times12/28/11, 4/3/12, 8/7/12

Red is at Highest Value of CRPBlue is the Day After End of Antibiotic/Prednisone Therapy

Green is Four Months Later


Closeup of Uncommon LS Microbes12/28/11 Stool Sample

45xReduced

By Therapy

90xReduced

By Therapy

8%Increased

By Therapy

Two separate research teams

have found strikingly high concentrations

of Fusobacterium in tumor samples

collected from colorectal cancer

patients.October 18, 2011

From War to Gardening

“I would like to lose the language of warfare,” said Julie Segre, a senior investigator at

the National Human Genome Research Institute. ”It does a disservice to all the bacteria

that have co-evolved with us and are maintaining the health of our bodies.”

DIY Systems Biology -Toward P4 Healthcare

Download pdfs from Journal:

Over 1000 Downloads So Far

http://onlinelibrary.wiley.com/doi/10.1002/biot.201100495/full

Integrative Personal Omics ProfilingReveals Details of Clinical Onset of Viruses and Diabetes

• Michael Snyder, Chair of Genomics Stanford Univ.

• Genome 140x Coverage

• Blood Tests 20 Times in 14 Months– tracked nearly

20,000 distinct transcripts coding for 12,000 genes

– measured the relative levels of more than 6,000 proteins and 1,000 metabolites in Snyder's blood

Cell 148, 1293–1307, March 16, 2012

janssen immune system_&_microbiome_022213 (1)

Documents

stool variables

diseaseblood variables

peak crp

peak lactoferrin

jolla research

dna snps

body data

data points