L5: Gut Microbiome and Cancer and Cancer Immunotherapy (D. Philpott)

Question 1

microbiome

Answer 1

theatre of activity + community of microorganisms

Question 2

microbiota

Answer 2

assemblage of microorganisms present

Question 3

largest diversity and number of bacetria

Answer 3

colon
2 main phyla: Firmicutes and Bacteroidetes

Question 4

development of microbiota

Answer 4

fetus sterile until birth
vaginal delivery vs cesarean delivery dictate which type of organisms first colonize the infant
infant: milk consumption and solid food introduction
toddler: full adult diet –> adult-like microbiota

Question 5

dysbiosis

Answer 5

altered microbiota - associated with disease
compositional and functional changes
IBS, GI cancers, T1Diabetes, infectious disease, T2Diabetes, obesity, atherosclerosis

Question 6

factors that might impact microbiota composition

Answer 6

diet, lifestyle, antibiotics, hygiene

Question 7

how do we assess composition of microbiota

Answer 7

through 16s rRNA amplicon sequencing
16s rRNA is the RNA portion of the ribosome - highly conserved in all bacteria (specific to bacteria) V4 region, PCR
this can help us understand which gene is associated with which bacteria

Question 8

metagenomic shotgun sequencing

Answer 8

more expensive but more info about functionality of microbiome
take fecal matter - sequence everything

Question 9

using germ-free mice to study contribution of microbiota to host health and disease

Answer 9

born and raised in sterile conditions, HEPA filter
have a tendency to consume more calories, weigh less (bacteria important for breaking down food), live longer
very little IgA, no development of GALT, very few T cells

Question 10

role of microbiota in allogeneic hematopoietic stem cell transplantation

Answer 10

simpson index high diversity correlated with survival for patients with blood cancers

Question 11

simpson index, alpha diversity

Answer 11

a measure of how well represented each taxon is relative to others
high diversity = healthy microbiota

Question 12

role of microbiota in allogeneic hematopoietic stem cell transplantation: use of antibiotics

Answer 12

decreased diversity = greater mortality

Question 13

ICI (Immune checkpoint inhibitors) efficacy correlates with…

Answer 13

mutation burden
high levels of PD-L1 expression
profile of gut microbiota

Question 14

cancer patients treared with ICI got antibiotics

Answer 14

led to decreased OS

Question 15

role of the microbiota in anti-PDL1 cancer therapy

Answer 15

JAX microbiome has a specific abundance –> associated with greater CD8 T cell infiltration of tumors

Question 16

role of microbiota in anti-CTLA4 cancer therapy

Answer 16

Didn’t work in germ-free mice= microbes are crucial for efficacy of therapy
Antibiotics similarly reduced efficacy of anti-CTLA4

Question 17

role of microbiota in humans treated with ICIs

Answer 17

Transfer of responder microbiota compared to nonresponder microbiota into germ-free mice correlates with response to anti-PD1
Greater CD4/ fewer Tregs in tumors
Prove causation of these microbes of promoting efficacy of cancer therapy

Question 18

how do microbes impact ICI outcomes - caveats with microbial studies

Answer 18

Increase levels of CD8 + T cells
Alterations of tumor microenvironment (bacterial translocation and infiltration of tumor)
Cross reactive antigens (anticancer or antimicrobial T cell response boosts ICIs)

Question 19

ways to modulate gut microbiota to improve ICI outcomes

Answer 19

Fecal microbial transplants
Probiotics/ bacteria consortia
Pre-biotics -metabolites for bacteria to break down complex carbohydrates
Postbiotics

Question 20

knowing that microbiome affects tumor progression, describe the strategy to mitigate any microbial effects on your animal experiments. How would you ensure your strategies worked

Answer 20

• Co-house animals
• Give antibiotic treatment then FMT for desired microbiome
• Do 16S rRNA sequencing/shotgun sequencing to ensure microbiomes are the
  same from each mouse strains