Microbiome as a marker for

CRC screening

Dr Sunny H WongMBChB (Hons), DPhil, MRCP, FHKCP, FHKAM (Medicine)

Assistant Professor

Institute of Digestive Disease

Department of Medicine and Therapeutics

WEO CRC Screening

Committee Meeting

Global burden of CRC

Incidence:

2nd cancer in female (~614 000)

3rd cancer in male (~746 000)

Mortality: 4th cancer (~694 000)

WHO 2015 and World Cancer Report 2014

Rationale of CRC screening

APC / KRAS Smad2/4 p53

Up to 10 years – can we catch it?

Screening reduces mortality

Jemal et al, Cancer J Clin 2008

Zauber et al, NEJM 2012

Before screening After screening

Colonoscopy is good, but…

• Requires expertise and high cost

• Bowel preparation

• Small but definite risk

• Patient preference

There is a need for non-invasive

screening biomarkers

Fecal occult blood markers

Guaiac fecal-occult blood test

(gFOBT)

• Detects heme

• Limited by

– Limited sensitivity (37-79%)

– Imperfect specificity

– Need for dietary restriction

Faecal immunochemical test

(FIT)

• Specific antibodies to globin

• Performance

– Sensitivity for CRC - 66-88%

– Sensitivity for AN - 27-54%

– Specificity 90-95%

• More specific for LGI bleeding

• Data across populations

Allison et al, NEJM 1996

Levi et al, Ann Intern Med 2007

Morikawa et al, Gastroenterology 2005

Wong et al, Aliment Pharmacol Ther 2003

Van Rossum et al, Gastroenterology 2008

Molecular markers

• DNA (genomic / metagenomic)

– SNPs, chromosomal aberration, microsatellite instability

– microbial markers

• RNA (transcriptomic)

– mRNA, micro-RNA

• Protein and metabolite

(proteomic / metabolomics)

– tumor antigens, metabolites

• Others

– epigenetic methylation

Types and clinical uses

RATIONALE

Using the microbiome as marker

CRC and microbiome

Enterotoxigenic Bacteroides fragilis

Wu S et al, Nat Med 2008 Goodwin et al, PNAS 2011

SPF Apc+/min

Enterotoxigenic

Genotoxic Escherichia coli

AOM il10-/- modelGenotoxic

Arthur et al, Science 2012

Fusobacterium nucleatum

Kostic et al, Cell Host Microbe 2013 Rubinstein et al, Cell Host Microbe 2013

Myeloid DC

Abed J et al, Cell Host Microbe 2016 Yang Y et al, Gastroenterology 2017

Fusobacterium nucleatum

• Enriched in cases

– Fusobacterium nucleatum

– Peptostreptococcus stomatis / anaerobius

– Parvimonas micra

– Solobacterium moorei

– Clostridium hathewayi

Yu, Gut 2015 Yu et al, Gut 2015

Oral pathogen network

Oral pathogens

Yu et al, Gut 2015

Nakatsu et al, Nat Commun 2015

CRC microbiota – cause or effect?

Wong et al, Gastroenterology 2017

Effects of CRC stools

Wong et al, Gastroenterology 2017

COLORECTAL CANCER

Using the microbiome as marker

Microbial marker panel

2.1 million microbial genes

140,455 genes associated with disease status

(p<0.01, FDR=11%)

20 genes identified by

mRMR feature selection method

CRC index of log

abundance

Yu et al, Gut 2015

Microbial marker panel

Classifier of 22 speciesAUC metagenome = 0.84AUC clinical score = 0.63

Zeller et al, Mol Syst Biol 2014

Microbial marker panel

Zackular JP et al, Cancer Prev Res 2014

Microbial marker panel

Liang et al, Clin Cancer Res 2016

Fusobacterium nucleatum (Fn)

• Relative abundance of

three bacteria in 309 +

181 subjects

• Three bacteria

including

Fusobacterium

nucleatum (Fn)

Wong et al, Gut 2017

Abundance in controls

and colorectal cancer patients

Performance of Fn marker

Wong et al, Gut 2017

Improve performance of FIT

Salvage missed tumors

• Combining FIT with Fn

increases its detection rates for

CRC to a sensitivity of 92.3%

• The combined test salvages

more than 75% of the CRC

samples missed by FIT alone

Fn as a marker for CRC

• Kostic et al, Cell Host Microbe 2013

• Wu et al, Microb Ecol 2013

• Anh et al, J Natl Cancer Inst 2013

• Zeller et al, Mol Syst Biol 2014

• Zackular et al, Cancer Prev Res 2014

• Flanagan et al, Eur J Clin Microbiol Infect Dis 2014

• Goedert et al, EBioMedicine 2015

• Yu et al, Gut 2015

• Shah et al, Gut 2016

• Liang et al, Clin Cancer Res 2016

• Wong et al, Gut 2017

• Suehiro et al, Ann Clin Biol 2017

• Ekolf et al, Int J Cancer 2017

Are we aiming right?

ADENOMA

Using the microbiome as marker

Can we use Fn for adenoma?

Kostic et al, Cell Host Microbe 2013 Zeller et al, Mol Syst Biol 2014

Fn marker for advanced adenoma

AUC - 0.56 (FIT), 0.59 (Fn)

0.65 (combined)

It’s a long way

http://www.molecularmedicineireland.ie/

We are here Hopeful, but need to look ahead

It is fruitful – FDA approved markers

Challenges with microbial markers

1. Challenges with the unknowns

Daily fluctuations

Food, antibiotics

Effects of diseases and drugs

Ethnic differences

2. Screening setting unknown

3. Feasibility and convenience in use

Thank you

• Cheong Chow

• Dr Thomas Kwong

• Dr Jessie Liang

• Professor Jun Yu

• Professor Joseph Sung