Emerging Trends and
Provocative Findings in
Basic Science
NASPGHAN 2014
John Barnard, MD
DISCLOSURE
No disclosures relevant
to this presentation.
• Big Data
• Misconduct
• CRISPR-Cas9
• Liver stem cells
• Microbiome
• Genomics
Big Data
Big data is an allencompassing term for
any collection of data sets
so large and complex that
it becomes difficult to
process using traditional
data processing
applications.
volume
variety
velocity
variability
PubMed Citations with “Big Data” in Title
200
150
100
50
0
Scholarship
in theHepatol
Networked
Nat Rev Gastroenterol
6:386, 2014 World: Big
Data, Little Data, No Data
Christine L. Borgman, University of
California, Los Angeles
Oliver Smithies Lecture, Balliol College,
Oxford. Oxford, UK. Jun. 2013.
Why Hasn’t ‘Big Data’ Saved Democracy?
Large clinical data sets
Payer data sets
Microbiome data*
Image data
Will Big Data Legitimize
the Field of Motility?
EHR data
J Fuzzy Science
Genomic
data*2014?
Sensor data
Proteomic data
By Fred Barbash
July 29, 2014
CRISPR-Cas9: Gene Editing
• Bacterial immunity against foreign DNA
• CRISPRs
 clustered regularly interspaced short
palindromic repeats)
 “RNA guide”
• Cas9
•
 Endonuclease
 “molecular scissors”
CRISPR-Cas9 system is “simple and efficient”
And many
others
“Genome editing
has never been
easier”
Netherlands
2 children with
DF508 CFTR mutation
Summary
The CRISPR/Cas9 system
edits the genome
in intestinal stem cells organoids
and
restores CFTR function.
Background and Methods
adult mice
on NTBC
Results
Results
Summary
First proof of principle
that CRISPR-Cas
corrects a genetic disease in vivo
Only 1/250 hepatocytes corrected,
aided by positive selection
by NTBC removal.
• One cell embryo injection
• Modification of two genes
(Rag1 and PPARg)
History’s path is unchartable
when it is not yet past
but present,
when we are still standing
in the middle of it.
Jennifer Couzin-Frankel
Science 342:1432, 2013
Implications of CRISPER-Cas9
• Genome editing is easy?
• Promising
• Correction of single
gene disorders
is genuinely
possible
A Comprehensive Review
Cell 157, 1324-1338, 2014
Background
• Hippo/YAP signaling pathway
– highly conserved, complex signaling pathway
– brake on cell proliferation/organ size
– tumor suppressor signaling
– important in regulation of liver size
Background
YAP
ductal cell
YAP
HIPPO
hepatocytes
Oval cells
(Progenitor cells)
AAV-YAP
Implications
Sci Trans Med 2014; 6:245, 1-21.
J Clin Invest 2014 124:3617
Background and Methods
• RISK study (CCFA)
• Large inception pediatric IBD cohort
– N = 1656, over 28 sites
– Treatment naïve; Prospective
– Ileal host gene expression, microbial
abundance and deep phenotyping in 359
subjects (controls, ileocolonic, colon-only
and UC)
Results
Ileocolonic
Crohn’s
Colon only
Crohn’s
UC
1281 ileal
host genes
1.5 X
vs controls
1055 ileal
host genes;
82%
similar to
ileocolonic
232 ileal
host genes;
18%
similar to
ileocolonic
Results
NL ileum
UC
colon only
Crohn’s
ileocolonic
Crohn’s
Host gene expression
and microbial shifts in ileal IBD.
Summary
• Ileal host gene expression is
remarkably similar in patients with
ileocolonic Crohn’s disease and
colon-only disease
• Host gene and microbe profiles
identify ileum as primary inductive
site for all forms of Crohn’s disease
Background and Methods
• RISK study, CCFA
• N = 447 Crohn’s & 221 controls (28 sites)
– Treatment naïve
– Prospective
• Mucosa-associated and lumenal
microbiota 16S rRNA sequencing along
with deep phenotyping
Results
Most prominent
microbiome changes
are in tissue
associated microbiota
Antibiotic exposure
amplifies dysbiosis
Results
Of those bacteria
increased in Crohn’s –
the more dramatic the
increase; the higher the
PCDAI (and converse)
Microbiota
Dysbiosis Index (MDI)
predicts PCDAI
PCDAI
Results
Sensitivity
Biopsy-associated
ilieal microbiome is
most accurate for
disease classification
1 - Specificity
Predictive modeling
for relapse using
microbiome and
clinical variables
better than clinical
variables alone
Summary
• Microbiome at diagnosis strongly
correlates with Crohn’s disease status
• Antibiotics aggravate dysbiosis
• Mucosa-associated microbiome may be
better than lumenal in assessing disease
parameters
Mice given E coli engineered to produce
known anorexogenic lipids
Healthy Mice
TallyHo Obese Mice
Room Source
antibiotics
biocides
Premie
Science 2014; 345:1048-1052
Summary
• Seven families over 6 weeks
– “Home Microbiome Project”
– Human and home microbiome (including some pets)
• Home microbiome comes from human occupants
• Home identifiable knowing human microbiome
• Occupant leaving home for even three days begins
to redefine home microbiome
• … other disturbing observations and implications…
Nat Genet 2014; 46:1131-1134
Summary
• IBD patients GWAS
– 172 with pancreatitis within 3 mos of 6-MP
– 2035 IBD no pancreatitis (controls)
– 472 IBD on 6-MP – no pancreatitis (replication)
• HLA DQA1 HLA DRB1
– Heterozygotes: 9% risk of pancreatitis
– Homozygotes: 17% risk of pancreatitis