Measuring the Human Brain-Gut Microbiome-Immune System Dynamics: a Big Data Challenge

“Measuring the Human Brain-Gut Microbiome-Immune System Dynamics: a Big Data Challenge”

Plenary Talk

45th Annual Meeting of the Behavior Genetics Association

San Diego, CA

June 18, 2015

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.net1

June 8, 2012 June 14, 2012

Interest in the Human MicrobiomeHas Moved Quickly From Frontier Science to Public Awareness

August 18, 2012June, 2012

To Understand the Interaction of Genetics and Human BehaviorWe Must Consider the Human Microbiome

Your Microbiome is Your “Near-Body” Environment

and its CellsContain 300x

as Many DNA GenesAs Your Human Cells

Your Body Has 10 Times As Many Microbe Cells As Human Cells

The Microbiome–Gut–Brain AxisProvides New Systemic Insights into Shifts in Behavior and Disease

Source: Montiel-Castro, et al. Frontiers in Integrative Neuroscience 2013

Many New Research Studies are Demonstrating Deep Relationships Between the Gut Microbiome and Behavioral Disorders

Gut Microbes Regulate Serotonin Production,90% of Which is in the Large Intestine

“It's almost unthinkable that the gut is not playing a critical role in mind states,"

says gastroenterologist Emeran Mayer, MD, director of the Center for Neurobiology of Stress at UCLA

Cell 161 264-276 (2015)

How Can One Combine Human Genetic GWASWith Gut Microbiome Metagenomics and Immune System Dynamics?

An N=1 Case Study of an Autoimmune Disease

I Have Turned My Body into a Genomic and Biomarker Observatory

One Blood DrawFor MeCalit2 64 Megapixel VROOM

Only One of My Blood Measurements Was Far Out of Range--Indicating Chronic Inflammation

Normal Range <1 mg/L

27x Upper Limit

Complex Reactive Protein (CRP) is a Blood Biomarker for Detecting Presence of Inflammation

Episodic Peaks in Inflammation Followed by Spontaneous Drops

Adding Stool Tests RevealedOscillatory Behavior in an Immune Variable Which is Antibacterial

Normal Range<7.3 µg/mL

124x Upper Limit for Healthy

Lactoferrin is a Protein Shed from Neutrophils -An Antibacterial that Sequesters Iron

TypicalLactoferrin Value for Active Inflammatory

Bowel Disease (IBD)

I Turned to SNP Analysis and GWAS to Understand My Human Genomic Predispositions

I Found I Had One of the Earliest Known SNPsAssociated with Crohn’s Disease

From www.23andme.com

SNPs Associated with CD

Polymorphism in Interleukin-23 Receptor Gene

— 80% Higher Risk of Pro-inflammatoryImmune Response

rs1004819

NOD2

IRGM

ATG16L1

There May Be a Correlation Between CD SNPsand Where and When the Disease Manifests

Me-MaleCD Onset

At 60-Years Old

Female CD Onset

At 20-Years Old

NOD2 (1)Rs2066844

2.08x Increased Risk

Il-23RRs1004819

1.8x Increased Risk

Subject withIleal Crohn’s

Subject withColonic Crohn’s

Source: Larry Smarr and 23andme

I Also Had an Increased Risk for Ulcerative Colitis,But a SNP that is Also Associated with Colonic CD

I Have a 33% Increased Risk for Ulcerative Colitis

HLA-DRA (rs2395185)

I Have the Same Level of HLA-DRA Increased Risk

as Another Male Who Has HadUlcerative Colitis for 20 Years

“Our results suggest that at least for the SNPs investigated [including HLA-DRA],

colonic CD and UC have common genetic basis.”-Waterman, et al., IBD 17, 1936-42 (2011)

So IBD May be Stratified by a Personalized Combinationof the 163 Known SNP Loci Associated with IBD

The width of the bar is proportional to the variance explained by that locus

“Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease,” Jostins, et al. Nature 491, 119-124 (2012)

Could Changes in the Microbiome Ecology and Genetic StructureProvide Some of the Missing Variance?

However, the Total Disease Variance Explained Is Only:• 13.6% for Crohn’s• 7.5% for Ulcerative Colitis

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) 

I Have Been Quantifying All Three

The Genetic Distance Between MicrobesVastly Exceeds That Among All Animals and Plants

You Are

Here

Source: Carl Woese, et al

Tree of Life Derived from 16S rRNA Sequences

For Deep Analysis of Changes in the Gut Microbiome EcologyOur Team Compared a Healthy Population with 3 Types of IBD

5 Ileal Crohn’s Patients, 3 Points in Time

2 Ulcerative Colitis Patients, 6 Points in Time

“Healthy” Individuals

Source: Jerry Sheehan, Calit2Weizhong Li, Sitao Wu, CRBS, UCSD

Total of 27 Billion ReadsOr 2.7 Trillion Bases

Inflammatory Bowel Disease (IBD) Patients

250 Subjects1 Point in Time

7 Points in Time

Each Sample Has 100-200 Million Illumina Short Reads (100 bases)

Larry Smarr(Colonic Crohn’s)

From Swedish Twin Study

To Map Out the Dynamics of Autoimmune Microbiome Ecology Couples Next Generation Genome Sequencers to Big Data Supercomputers

Illumina HiSeq 2000 at JCVI

SDSC Gordon Data Supercomputer

Example: Inflammatory Bowel Disease (IBD)

We used 25 CPU-yearsto compute

comparative gut microbiomesstarting from

7 trillion DNA bases of my samples,

255 healthy, and 20 IBD controls

Computational NextGen Sequencing Pipeline:From Sequence to Taxonomy and Function

PI: (Weizhong Li, CRBS, UCSD): NIH R01HG005978 (2010-2013, $1.1M)

When We Think About Biological DiversityWe Typically Think of the Wide Range of Animals

But All These Animals Are in One SubPhylum Vertebrataof the Chordata Phylum

All images from Wikimedia Commons. Photos are public domain or by Trisha Shears & Richard Bartz

Think of These Phyla of Animals When You Consider the Biodiversity of Microbes Inside You

All images from WikiMedia Commons. Photos are public domain or by Dan Hershman, Michael Linnenbach, Manuae, B_cool

PhylumAnnelida

PhylumEchinodermata

PhylumCnidaria

PhylumMollusca

Phylum Arthropoda

PhylumChordata

We Found Major State Shifts in Microbial Ecology PhylaBetween Healthy and Three Forms of IBD

Most Common Microbial

Phyla

Average HE

Average Ulcerative Colitis

Average LSColonic Crohn’s Disease

Average Ileal Crohn’s Disease

Collapse of BacteroidetesExplosion of Actinobacteria

Explosion of Proteobacteria

Hybrid of UC and CDHigh Level of Archaea

Dell Analytics Separates The 4 Patient Types in Our DataUsing Our Microbiome Species Data

Source: Thomas Hill, Ph.D.Executive Director Analytics

Dell | Information Management Group, Dell Software

Healthy

Ulcerative Colitis

Colonic Crohn’s

Ileal Crohn’s

I Built on Dell Analytics to Show Dynamic Evolution of My Microbiome Toward and Away from Healthy State – Colonic Crohn’s

Healthy

Ileal Crohn’s

Seven Time Samples Over 1.5 Years

Colonic Crohn’s

This Year We Will Extend My Stool Time SeriesCollaborating with the UCSD Knight Lab

Larry’s 40 Stool Samples Over 3.5 Years to Rob’s lab on April 30, 2015

Time Series Reveals Behavior Changes (Depression, Malaise)Associated with Time Progression of Autoimmune Disease

Immune &Inflammation

Variables

Weekly Symptoms

PharmaTherapies

StoolSamples

Mood Disorders

2009 20142013201220112010 2015

In a “Healthy” Gut Microbiome:Large Taxonomy Variation, Low Protein Family Variation

Source: Nature, 486, 207-212 (2012)

Over 200 People

We Computed the Relative Abundance of Microbial Gene Families -~10,000 KEGG Orthologous Genes, Across Healthy and IBD Subjects

How Large is the Microbiome’s Genetic ChangeBetween Health and Disease States?

Ratio of One of the Healthy Subjects to the Average KEGG for 35 Healthy:Test to see How Much Inter-Personal Variation There is Within Healthy

Most KEGGs Are Within 10xOf Healthy for a Random HE

Ratio of Random HE11529 to Healthy Average for Each Nonzero KEGG

Nonzero KEGGs

We Computed the Relative

Abundance of 10,000 KEGGsin 35 HealthyAnd 25 IBD

Patients

However, Our Research Shows Large Changes in Protein Families Between Health and Disease

Most KEGGs Are Within 10xIn Healthy and Ileal Crohn’s Disease

KEGGs Greatly IncreasedIn the Disease State

KEGGs Greatly DecreasedIn the Disease State

Over 7000 KEGGs Which Are Nonzero in Health and Disease States

Ratio of CD Average to Healthy Average for Each Nonzero KEGG

Note Hi/LowSymmetry

Note 700 KEGGsWith Ratio >10

Note 1000 KEGGsWith Ratio <0.1

Next Step: Compute Genes and Function For All ~300 People’s Gut Microbiome

Full Processing to Function:Genes & Protein Families

(COGs, KEGGs)

Would Require ~1-2 Million Core-Hours

UC San Diego Will Be Carrying Out a Major Clinical Study of IBD Using These Techniques

Inflammatory Bowel Disease BiobankFor Healthy and Disease Patients

Drs. William J. Sandborn, John Chang, & Brigid BolandUCSD School of Medicine, Division of Gastroenterology

Already 185 Enrolled

Announced November 7, 2014!

We Must Move From Combating Single Microbe Diseases to Developing the Human/Microbiome System Approach to Public Health

Bach (2002) N Engl J Med, Vol. 347, 911-920

2014For Public Health It is Still About Microbes,But from Single Species to Entire Ecologies

The United States Population’s Human Gut MicrobiomeHas Diverged a Great Deal from Hunter-Gatherers

“The microbiome of uncontacted Amerindians,” J. C. Clemente, et al. Science Advances 1, e1500183 (2015).

[Amerindians in Venezuela/Columbia]

[Africa]

HumanMicrobiomeProject

Missing Microbes

The Coupled Neural, Immune, and Microbiome SystemsProvide a Model Explaining How Nutrition Can Alter Neurodevelopment

Thanks to Our Great Team!

UCSD Metagenomics TeamWeizhong LiSitao Wu

Calit2@UCSD Future Patient TeamJerry SheehanTom DeFantiKevin PatrickJurgen SchulzeAndrew PrudhommePhilip WeberFred RaabJoe KeefeErnesto Ramirez

AyasdiDevi RamananPek Lum

JCVI TeamKaren NelsonShibu YoosephManolito Torralba

SDSC TeamMichael NormanMahidhar Tatineni Robert Sinkovits

UCSD Health Sciences TeamRob KnightWilliam J. SandbornElisabeth EvansJohn ChangBrigid BolandDavid Brenner

Dell/R SystemsBrian KucicJohn Thompson