Emerging Trends and Provocative Findings in Basic Science NASPGHAN 2014 John Barnard, MD

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Big Data Misconduct CRISPR-Cas9 Liver stem cells Microbiome Genomics

Big Data Big data is an all- encompassing term for any collection of data sets so large and complex that it becomes difficult to process using traditional data processing applications.data sets volume variety velocity variability

PubMed Citations with “Big Data” in Title

Will Big Data Legitimize the Field of Motility? J Fuzzy Science 2014? Scholarship in the Networked World: Big Data, Little Data, No Data Christine L. Borgman, University of California, Los Angeles Oliver Smithies Lecture, Balliol College, Oxford. Oxford, UK. Jun Why Hasn’t ‘Big Data’ Saved Democracy? Nat Rev Gastroenterol Hepatol 6:386, 2014 Large clinical data setsEHR data Payer data setsGenomic data* Microbiome data*Sensor data Image dataProteomic 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  F508 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

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 PPAR  )

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, , 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 HIPPO hepatocytes YAP ductal cell Oval cells (Progenitor cells) YAP AAV-YAP

Sci Trans Med 2014; 6:245, Implications

J Clin Invest :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 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 Host gene expression and microbial shifts in ileal IBD. NL ileum UC colon only ileocolonic Crohn’s Crohn’s

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 Microbiota Dysbiosis Index (MDI) predicts PCDAI PCDAI

Results Biopsy-associated ilieal microbiome is most accurate for disease classification Predictive modeling for relapse using microbiome and clinical variables better than clinical variables alone 1 - Specificity Sensitivity

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 Premie biocides antibiotics

Science 2014; 345:

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:

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