the human microbiome and colorectal cancer · quality control standards to evaluate reproducibility...
TRANSCRIPT
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The human microbiome and colorectal cancer
Emily Vogtmann, PhD, MPH
Research Fellow
Metabolic Epidemiology Branch
Division of Cancer Epidemiology & Genetics
April 20, 2017
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Outline
Introduction to the human microbiome Technologies to assess the microbiomeHuman microbiome and colorectal cancer Future directions
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Outline
Introduction to the human microbiome Technologies to assess the microbiomeHuman microbiome and colorectal cancer Future directions
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Microbiota and the tree of life
Microbes Bacteria Archaea Fungi Protists Viruses
Microbiome: collection of microbial genes
Kutschera (2011) Biol Direct & Pace (1997) Science
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Alpha and beta diversity
Forest 1 Forest 2
Alpha diversity = 3 Alpha diversity = 6
Alpha diversity• Counts (Taxonomy/OTUs)• Shannon index• Simpson index• Chao1• PD tree
Beta diversity• Bray-Curtis• UniFrac
Beta diversity2 shared5 different
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PCoA plot: Clustering by body site
The Human Microbiome Project Consortium (2012) Nature
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Outline
Introduction to the human microbiome Technologies to assess the microbiomeHuman microbiome and colorectal cancer Future directions
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History of microbial research
Image: http://learn.genetics.utah.edu/content/microbiome/study/
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Present day study
Images from: http://legacy.owensboro.kctcs.edu/gcaplan/anat2/study%20guides/apii%20study%20guide%20k%20digestive%20anatomy.htm, http://davidql.github.io/scope_talk/emoji_poop.png, http://dnatech.genomecenter.ucdavis.edu/wp-content/uploads/2013/10/Miseq.png, and reproductions from Morgan XC et al. (2012) PLoS Comp Biol
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Fecal collection methods
No Solution RNAlater 95% Ethanol
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Stability
Vogtmann, et al (2017) AJE
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Accuracy
Vogtmann, et al (2017) AJE
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Outline
Introduction to the human microbiome Technologies to assess the microbiomeHuman microbiome and colorectal cancer Future directions
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Colorectal cancer worldwide
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Meat and colorectal cancer
Cancer Research UK (http://gloriousnutrition.co.uk/processed-meat-popularity-decreasing-due-to-cancer-link/)
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Meat and the gut microbiome
David et al (2014) Nature
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Microbiome and colorectal cancer (U.S.)
Ahn et al (2013) JNCI
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Microbiome and colorectal cancer (U.S.)
Ahn et al (2013) JNCI
Case enrichment
• Fusobacterium
• Veillonellaceae• Anaerovorax
• Porphyromonas
• Atopobium
Control enrichment
• Firmicutes overall• Lachnospiraceae
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Meta-analysis of 16S rRNA gene studies
Shah et al (2017) Gut
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Meta-analysis of 16S rRNA gene studies
Shah et al (2017) Gut
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Potential mechanisms
Drewes et al (2016) BJC
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Conclusions
There is promise for fecal microbial markers to enhance FOBT or FIT tests for colorectal cancer screening
All previous studies have been cross-sectional
Prospective studies (and studies with multiple serial samples) are needed to understand microbial associations with colorectal cancer etiology
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Outline
Introduction to the human microbiome Technologies to assess the microbiomeHuman microbiome and colorectal cancer Future directions
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Future directions
Optimization of collection method for multiple technologies
Collect fecal samples in prospective cohort studies
Quality control standards to evaluate reproducibility
Standardization of methods for extraction, sequencing, and bioinformatics for data pooling and meta-analyses
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Acknowledgements DCEG Metabolic Epidemiology Branch
Christian Abnet
Gwen Murphy
Rashmi Sinha
DCEG Biostatistics Branch
Jianxin Shi
Xing Hua
Yunhu Wan
DCEG Cancer Genomics Research Laboratory
Belynda Hicks
Amy Hutchinson
Kristie Jones
Casey Dagnall
Shalabh Suman
Bin Zhu
University of Maryland
Owen White
UCSD
Rob Knight
Amnon Amir
University of Guelph
Emma Allen-Vercoe
Mayo Clinic
Nicholas Chia
Jun Chen
Heidi Nelson
Harvard University
Curtis Huttenhower
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www.cancer.gov www.cancer.gov/espanol