Table 1 Differentially expressed genes in Caco-2 cells following their HuMiX-based co-culture with LGG in comparison with in vivo data.

From: A microfluidics-based in vitro model of the gastrointestinal human–microbe interface

Gene

In vitro HuMiX-based co-cultures

In vivo data

Function

 

LGG culture conditions

Expression

logFC

P value

Subject

Expression

Reference

 

EGR1

Only differentially expressed when LGG growing under anaerobic conditions

Down

−2.56

0.0012

Human

Down

33

Transcription regulation, transcription factor activity for the regulation of cell proliferation and apoptosis, anti-cancer effect and IL-8 suppression

CCL2

 

Up

+1.51

0.0005

Human

Up

32

Chemotactic factor that attracts monocytes and basophils and binds to the chemokine receptors CCR2 and CCR4

SLC9A1

 

Down

−0.29

0.0168

Human

Down

32

Signal transduction, regulation of pH homeostasis, cell migration, cell volume and anti-inflammatory effect

UBD

 

Up

+0.61

0.0261

Human

Up

33

Proteasomal degradation, cytokine response, antimicrobial response and apoptosis

ELF3

Differentially expressed when LGG growing under both anaerobic and aerobic conditions

Up

+0.55

0.0022

Human & GF Piglet

Down

33, 34

ets family member, epithelial-specific function, transcriptional mediator of angiogenesis during inflammation and epithelial cell differentiation

CXCR4

 

Up

+0.94

0.0019

Human

Up

33

Chemotaxis, cell arrest, angiogenesis, cell survival, maintenance of the epithelial barrier function and HIV-1 co-receptor

MYBL2

 

Down

−0.26

0.0446

Human

Down

33

Anti-apoptopic function, regulation of cell cycle and transcription, and epithelial cell differentiation

PIM1

 

Up

+1.13

0.0039

Human

Up

32

Cell survival, cell proliferation, cell growth and signal transduction

CYP1A1

 

Up

+0.82

0.0090

Human

Up

33

Drug metabolism and xenobiotic transformation

GADD45B

 

Up

+0.60

0.0134

Human

Down

33

Cell growth and apoptosis

PILRB

 

Down

−0.45

0.0374

Human

Up

33

Receptors involved in the regulation of the immune system and cellular signalling

CDK9

 

Down

−0.22

0.0467

Human

Up

33

Cell proliferation, regulation of the cell cycle, and transcription elongation factor

SOX4

Only differentially expressed when LGG growing under anaerobic conditions

Down

−0.31

0.0295

GF piglet

Unspecified

34

Transcription factor, regulation of cell fate and apoptosis pathway, and prognostic marker in colon and gastric cancer

CEBPA

 

Up

+0.55

0.0172

GF piglet

Unspecified

34

Transcription factor, cell cycle regulation and regulation of metallothioneins

PTGS2

 

Up

+1.13

0.0145

GF piglet

Down

34

Prostaglandin biosynthesis and metabolism, inflammation, and mitogenesis

IGFBP2

 

Up

+0.5

0.015

GF piglet

Up

34

Regulation of IGF-mediated growth and developmental rates

GSTA1

 

Down

−0.5

0.005

GF piglet

Down

34

Detoxification of carcinogens, drugs, environmental toxins and products of oxidative stress

CTNNB1

 

Up

+0.54

0.003

GF piglet

Up

34

Regulation of cell growth in addition to the creation and maintenance of epithelial layers

TPD52

 

Up

+0.42

0.008

GF piglet

Up

34

Molecular marker in human cancer and target for immunotherapy

  1. FC, fold change; GF, germ free; LGG, Lactobacillus rhamnosus GG; IL-8, interleukin-8; IGF, insulin-like growth factor
  2. References indicating the functions of the highlighted genes are provided in Supplementary Table 12.
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