Table 1.
A summary of major statistically significant findings reported in this work
| Molecular subtype | IDICD (Immune-deficient infectious CD) |
S2FCD (senescence- and stress-induced fibrotic CD) | Approach | Comments | ||||
|---|---|---|---|---|---|---|---|---|
| Montreal classification | Penetrating (all) | NSNP (some) | Perianal (all) | Stricturing (few) | Stricturing (most) | NSNP (some) | RNA-seq analysis of CD PDOs vs. Healthy | N/A |
| Barrier integrity | Intact | Impaired | Intact | Intact in most, impaired in some | Intact in most, impaired in some | Impaired | TEER measurement ∗ FITC-dextran leakage ∗ |
∗ = HTP in 96-wells |
| Dysmorphic growth | No | Yes; defect in lumen formation | No | Yes; asymmetry, high cellularity | Yes; asymmetry, high cellularity | Yes | Light microscopy∗, IMARIS imaging∗ | ∗ = HTP in 96-wells |
| Apoptosis | High | Normal | NT | High (easily seen by H&E) | High | Normal | TUNEL assay# | # = LTP-semi-HTP in 8-wells |
| Apoptosis in response to TNF-α | High | High | NT | High | High | High | ||
| Proliferation | High | Normal | NT | High | High | normal | BrdU incorporation ∗ | ∗ = HTP in 96-wells |
| Ox DNA/RNA damage | Normal | High | NT | High | High | High | ELISA-based assay ∗ | ∗ = HTP in 96-wells |
| Crypt cell composition, differentiation | High crypt-axis score, high CEACAM7+ brush border cells, high goblet cells; defective MHC-II+ ISC-III, high goblet cells | Low crypt-axis score, defective MHC-II+ ISC-III, high goblet cells; defect in mitotic checkpoint. | RNA-seq | N/A | ||||
| Paneth cell dysfunction | Yes (excessive degranulation) | Yes (excessive degranulation) | Imaging (IF and EM) | LTP | ||||
| Goblet cell AMP production | Impaired severely | Reduced slightly | RNA-seq | N/A | ||||
| DNA damage (dsDNA break) | Normal | High | Flow cytometry (gH2AX) | LTP | ||||
| Senescence | Normal | High | SPIDER β-Gal assay, Flow cytometry | # = LTP-semi-HTP in 8-wells | ||||
| Bacterial clearance | Impaired | NT | Infection, lysis, plating and colony counting | LTP on EDMs | ||||
| Induction of ROS | High | Very high | ELISA ∗ | ∗ = HTP in 96-wells | ||||
| Microbe-challenged production of cytokines | Impaired | Normal | Multiplex ELISA assays (Mesoscale discovery) ∗ | ∗ = HTP in 96-wells | ||||
| Genotype-phenotype relationship | SNPs in genes within the bacterial clearance pathway, NOD2/ATG16L1 disease-driving SNPs, and SNPs in CRC-associated genes. | SNPs in the genes within the DNA damage-YAP-IL18 inflammatory pathway. | Genotyping ∗ and SNP analysis | HTP | ||||
NSNP, non-stricturing non-penetrating; ROS, reactive oxygen species; NT, not tested; HTP, high throughput; LTP, low throughput.