Gastrointestinal Organoid Biobank

Read about

• What are Patient Derived Organoids?
• Gastrointestinal Organoid Biobank
• Ordering Information for PDO Biobank
• Gastrointestinal Organoid Data

What are Patient Derived Organoids?

Patient derived organoids (PDOs) are novel in vitro 3D cell models that preserve original tissue physiology and molecular pathology, thus representing a clinically-relevant alternative to traditional 2D cell lines and an effective tool to refine and reduce animal models. PDOs can be derived from adult patient biopsies or resected tissues containing native LGR5+ stem cell populations and cultured within an ECM-rich substrate using specialized organoid media such as L-WRN conditioned media (SCM105). Adult tissue derived organoids are phenotypically and genetically stable in long term culture, presenting more mature phenotypes compared to iPSC-derived organoids. Importantly, PDOs have shown to be able to predict patient clinical responses to chemotherapeutic. 

Gastrointestinal Organoid Biobank

We are now offering a comprehensive biobank of highly characterized tissue-derived human gastrointestinal organoids from normal and diseased patients. The intestinal organoid biobank contains over 50 highly characterized intestinal organoids from both normal and diseased patients derived from multiple regions of the digestive systems including small intestine (duodenum, ileum), stomach, rectum and colon.

3dGRO^™ organoids were derived utilizing HUB Organoid Technology. The purchaser of this product shall agree to HUB’s terms of use, which shall be separately acknowledged and accepted by such purchaser, prior to transfer of this product to purchaser.

Biobank Overview

• 58 Patient Derived Organoid Samples
• Multiple Genders, Age, and Sex
• Multiple Tissues/Diseases: Colon, Duodenum, Ilium, Stomach, Rectum, Cancer, Ulcerative Colitis, IBS
• RNA-Seq Available
• Low Passage and High Viability
• Cultured in Optimized 3dGRO^™ L-WRN Conditioned Media

Prep-78-C (SCC311)

Prep-87-C (SCC321)

Prep-81-C (SCC313)

14-881-CR (SCC310)

Figure 1. Patient-derived colon organoids from both normal (SCC311, SCC321, SCC313) and diseased patients (rectal adenocarcinoma, SCC310) cultured in L-WRN conditioned media (SCM105) for five passages.

Ordering Information for PDO Biobank

Normal Gastrointestinal PDOs

ID	Catalog Number	Age	Sex	Organ	Disease Type or Normal
Prep 78-C	SCC311	52	F	Colon	Normal (RNA-seq)
Prep 80-C	SCC312	29	F	Colon	Normal (RNA-seq)
Prep 81-C	SCC313	49	F	Colon	Normal (RNA-seq)
Prep 81-D	SCC314	49	F	Duodenum	Normal (RNA-seq)
Prep 83-C	SCC315	45	F	Colon	Normal (RNA-seq)
Prep 83-D	SCC316	45	F	Duodenum	Normal (RNA-seq)
Prep 84-C	SCC317	56	F	Colon	Normal (RNA-seq)
Prep 84-D	SCC318	56	F	Duodenum	Normal (RNA-seq)
Prep 85-C	SCC319	62	F	Colon	Normal (RNA-seq)
Prep 85-D	SCC320	62	F	Duodenum	Normal (RNA-seq)
Prep 87-C	SCC321	21	M	Colon	Normal (RNA-seq)
Prep 87-D	SCC322	21	M	Duodenum	Normal (RNA-seq)
Prep 88-C	SCC323	33	F	Colon	Normal (RNA-seq)
Prep 88-D	SCC324	33	F	Duodenum	Normal (RNA-seq)
Prep 89-C	SCC325	55	M	Colon	Normal (RNA-seq)
Prep 89-D	SCC326	55	M	Duodenum	Normal (RNA-seq)
18-1417-N	SCC327	45	M	Colon	Normal (CRC tissue adjacent) (RNA-seq)
ht-099-C	SCC330	59	F	Colon	Normal (RNA-seq)
ht-101-C	SCC332	59	F	Colon	Normal (RNA-seq)
ht-103-C	SCC335	63	M	Colon	Normal (RNA-seq)
ht-104-C	SCC336	51	M	Colon	Normal (RNA-seq)
ht-104-I	SCC337	51	M	Ileum	Normal (RNA-seq)
ht-105-C	SCC338	19	M	Colon	Normal (RNA-seq)
ht-105-I	SCC339	19	M	Ileum	Normal (RNA-seq)
ht-118-C	SCC340	43	M	Colon	Normal
ht-119-C	SCC341	53	F	Colon	Normal
ht-127-S	SCC342	52	F	Stomach	Normal
ht-128-S	SCC343	60	F	Stomach	Normal
ht-129-S	SCC344	60	M	Stomach	Normal
ht-130-S	SCC345	68	M	Stomach	Normal
ht-215-CD	SCC346	59	F	Colon Descending	Normal
ht-215-CT	SCC347	59	F	Colon Transcending	Normal
ht-215-D	SCC348	59	F	Duodenum	Normal
ht-222-D	SCC349	33	M	Duodenum	Normal
ht-180-D	SCC350	38	F	Duodenum	Normal
ht-185-D	SCC351	45	M	Duodenum	Normal
ht-188-D	SCC352	50	F	Duodenum	Normal
ht-205-CS	SCC353	33	F	Colon Sigmoid	Normal Margin to Crohns (RNA-seq)
ht-205-D	SCC354	33	F	Duodenum	Normal Margin to Crohns
ht-205-I	SCC355	33	F	Ileum	Normal Margin to Crohns
ht-213-CA	SCC356	36	F	Colon Ascending	Normal margin to UC
ht-213-CD	SCC357	36	F	Colon Descending	Normal margin to UC
ht-213-CT	SCC358	36	F	Colon Transcending	Normal margin to UC
ht-213-D	SCC359	36	F	Duodenum	Normal margin to UC
ht-214-I	SCC360	46	M	Ileum	Normal margin to UC
ht-227-D	SCC362	62	M	Duodenum	Normal margin to UC
ht-230-D	SCC363	59	F	Duodenum	Normal margin to UC
ht-506-I	SCC368	34	F	Ileum	Normal Margin to Crohns
ht-352-D	SCC370	55	F	Duodenum	Normal
CSC.406N	SCC725	69	F	Colon	Normal (CRC tissue adjacent)
CSC.421N	SCC726	83	F	Colon	Normal (CRC tissue adjacent)
CSC.449N	SCC727	40	M	Colon	Normal (CRC tissue adjacent)

Adenoma and Adenocarcinoma Gastrointestinal PDOs

ID	Catalog Number	Age	Sex	Organ	Disease Type or Normal
14-881-CR	SCC310	46	M	Colon (Rectum)	Adenocarcinoma (TP53 Pro151Ser, KRAS Gly12Asp, APC Pro1443fs) (RNA-seq)
ht-131-C	SCC328	58	F	Colon	Adenoma
CSC.240	SCC721	83	M	Colon	Adenocarcinoma
POP.024.G4	SCC728	66	M	Colon	Adenocarcinoma, metastatic (liver)
CSC.073.G1	SCC729	67	M	Colon	Adenocarcinoma, metastatic (lung)
POP.074.G4	SCC730	86	M	Colon	Adenocarcinoma
POP.112.G2	SCC731	74	M	Colon	Adenocarcinoma
POP.161.G1	SCC732	60	F	Colon	Adenocarcinoma, metastatic (lung)
POP.141.G2	SCC733	57	M	Colon	Adenocarcinoma, metastatic (liver)
POP.174.G1	SCC734	56	M	Colon	Adenocarcinoma, metastatic (lung)
POP.170	SCC735	61	M	Colon	Adenocarcinoma, metastatic (liver)
POP.066.G4	SCC736	46	F	Colon	Adenocarcinoma, metastatic (liver)
POP.092.G2	SCC737	46	F	Colon	Adenocarcinoma
POP.160.G2	SCC738	69	M	Colon	Adenocarcinoma, metastatic (liver)
CSC.171C.G1	SCC739	47	F	Colon	Adenocarcinoma
CSC.171L.G1	SCC740	47	F	Colon	Adenocarcinoma, metastatic (liver)
CSC.413	SCC741	43	M	Colon	Adenocarcinoma
CSC.456	SCC742	68	M	Colon	Adenocarcinoma, metastatic (liver)
CSC.463	SCC743	43	F	Colon	Adenocarcinoma, metastatic (lung)

Colorectal Cancer Gastrointestinal PDOs

* Does not require HUB terms of use agreement prior to purchase.

ID	Catalog Number	Age	Sex	Organ	Disease Type or Normal
ISO34	SCC500*	N/A	N/A	Sigmoid Colon	Colorectal Cancer (APC ∆E1451*, BRAF ∆K601E)
ISO38	SCC501*	N/A	N/A	Sigmoid Colon	Colorectal Cancer (TP53 Pro151Ser, KRAS Gly12Asp, APC Pro1443fs)
ISO48	SCC502*	N/A	N/A	Caecum	Colorectal Cancer (PIK3CA ∆E542K, CTNNB1 ∆S33C)
ISO49	SCC503*	N/A	N/A	Lower Sigmoid Colon	Colorectal Cancer (APC ∆R1450*A1446Lfs*27, TP53 ∆R248Q, KRAS ∆G12D, PIK3CA ∆E542K, FBXW7 ∆R465C)
ISO50	SCC504*	N/A	N/A	Colon (Rectum)	Colorectal Cancer (APC ∆R232*E1286*, TP53 ∆R248Q", KRAS ∆G12D, SMAD4 ∆E526K, SMAD2 ∆S464*)
ISO57	SCC505*	N/A	N/A	Colon (Upper Rectum)	Colorectal Cancer (APC ∆Q978*, TP53 ∆R282W, KRAS ∆G13D)
ISO68	SCC506*	N/A	N/A	Sigmoid Colon	Colorectal Cancer (APC ∆Q1096*E1408*, TP53 ∆R248W, KRAS ∆G13D, SMAD4 ∆Q534*)
ISO72	SCC507*	N/A	N/A	Caecum	Colorectal Cancer (APC ∆Q1291*, KRAS ∆G12D, ERBB3 ∆A232V)

Crohn’s Disease and Ulcerative Colitis Gastrointestinal PDOs

ID	Catalog Number	Age	Sex	Organ	Disease Type or Normal
ht-206-CR	SCC365	24	F	Colon	Crohns (RNA-seq)
ht-206-I-CR	SCC366	24	F	Ileum	Crohns
ht-208-CR-CR	SCC367	23	M	Colon (Rectum)	Crohns (RNA-seq)
ht-506-I	SCC368	34	F	Ileum	Normal Margin to Crohns
ht-405-CA-UC	SCC369	36	F	Colon Ascending	Ulcerative Colitis

Gastrointestinal Organoid Data

Figure 2. Immunocytochemical characterization of human colon organoids (Colon-87, SCC321). Human colon PDOs are positive for colon-specific markers: CA II, CA IV and Mucin5B, posterior hindgut marker: CDX2, stem cell markers: Lgr5 and Sca1 and epithelial markers: TPH-1 and E-Cad.

Figure 3. Heatmap of top 30 differentially expressed genes.

Table 1. Gene expression differences of human iPSCs, iPSC derived colon organoids vs. adult patient derived tissue organoids.

hiPSC	Gene Name	Human iPSC (Average)	Patient-derived Colon Organoids (Average)	Human iPSC-derived Colon Organoids (Average)	Gene Characteristics
Genes Overexpressed in Colon Organoids Relative to hiPSC	TJP3	664	4932	4401	Tight Junction protein ZO-3
	CDKN1A	793	7570	11107	Cyclin dependent kinase inhibitor 1A
	EPHB2	784	2608	2372	Ephrin type B receptor 2
	ALDH1A1	64	6601	21930	Aldehyde Dehydrogenase 1
	LGR5	2	503	524	Intestinal stem cell biomarker
	MYC	1142	2828	2661	Proto-oncogene
	CDX2	4	1399	3980	Intestine-specific transcription factor
	KRT20	2	162	6027	Type 1 cytokeratin; major protein of mature enterocytes and goblet cells
	BMP2	169	827	2910	TGFb signaling pathway
	LY6E	2555	10162	36304	Associated with drug resistance & tumor immune escape in breast cancer
	EPHB3	61	4652	337	Ephrin type B receptor 3
	MUC5B	7	935	48	Encodes respiratory tract mucin glycoprotein
	MUC2	1	9	126	Secreted from goblet cells; gel provides insoluble mucous barrier to protect intestinal epithelium
	CA2	126	200	2207	Carbonic anhydrase II, enzyme expressed in many tissues, including GI tract
	CDH1	8052	10517	20622	Epithelial cadherin; E-cadherin
Lower Expressed Genes Relative to hiPSC	DCLK1	1942	4	2	Microtubule associated protein kinase; tuft cell marker in the small intestine
	CCNA2	4002	1226	1008	Cyclin A2
	TAGLN	4460	184	94	Actin cross-linking/gelling protein involved in Ca interactions and contractile properties of cell
	PLK1	5077	1513	1221	Early trigger for G2/M transition
	CDC20	5093	2198	1257	Involvement in pathway protein ubiquitination
	GNA14	711	9	74	G-protein family member

Figure 4. Adult tissue derived colon (SCC321, Colon-87) and duodenum (SCC320, DUO-85) organoids express SARS-CoV-2 related proteins ACE2 and TMPRSS2.

Figure 5. Forskolin-induced swelling of duodenum gut organoids (SCC314, DUO-81). The total organoid area increase relative to T=0 of FSK treatment was calculated and averaged from 10 individual cysts per condition. Scale bars = 500 um.

Figure 6. Generation of apical out illeum gut organoids (SCC339, HT-105-I). Apical out organoids were stained with dapi (blue) and ZO-1 (Green) antibodies to analyze efficiency of epithelial polarity reversion.