Table 2.

Genome engineering for applications of organoids

Categories	Genome Engineering Techniques	Organoid/Disease models	Results and phenotypes	Ref.
Fluorescence labeling	Electroporation with GFP/mCherry construct	Cerebral organoids	Live imaging of organoids	[155, 156]
	Electroporation with GFP construct	Retinal organoids	Live imaging of organoids	[157]
	GFP knock-in to TUBB locus with CRISPR-HOT	Hepatocyte organoids	Visualizing subcellular structures	[222]
Role of specific genes	CRISPR/Cas9-based knock-out of ODF2 and siRNA-based silencing of IFT88 in Sertoli cells	Testicular organoids	Loss of primary cilia, impaired formation of tubules	[159]
	CRISPR/Cas9-based knock-out of RB1 in hESC	Retinal organoids	Apoptosis, reduced number of retinal cells	[160]
	CRISPR/Cas9-based knock-out of Wnt4 in mESC	Kidney organoids	Lack of MET, impaired nephrogenesis	[161]
Modeling neurological disorders	Viral infection with mutant APPSL and PSEN1 (ΔE9)	3D neural culture (Alzheimer’s disease)	Elevation of amyloid-β, hyperphosphorylation of tau	[230]
	CRISPR/Cas9-based APOE4 variants in iPSCs	Cerebral organoids (Alzheimer’s disease)	Elevation of amyloid-β, hyperphosphorylation of tau	[163]
	Electroporation of Tau-P301S in iPSCs	Cerebral organoids (Frontotemporal dementia)	Hyperphosphorylation of tau	[164]
	CRISPR/Cas9-based genome editing (Δp35KI) in patient iPSCs carrying Tau-P301L	Cerebral organoids (Frontotemporal dementia)	Reduced phospho-tau and increased synaptophysin compared to patient iPSCs (Tau-P301L)	[165, 231]
	CRISPR/Cas9-based genome editing (LRRK2-G2019S) in iPSCs	Midbrain organoids (Parkinson’s disease)	Elevated aggregation of α-synuclein, increased expression of TXNIP	[166]
	Generation of patient iPSCs carrying LRRK2-G2019S	Midbrain organoids (Parkinson’s disease)	Reduced number and complexity of dopaminergic neuron, compensatory increase in FOXA2-positive progenitors	[167]
	Generation of iPSCs patients with idiopathic autism	Telencephalic organoids (Autism spectrum disorders)	Overproduction of inhibitory neurons, increased expression of FOXG1	[168]
	CRISPR/Cas9-based dosage reduction of FOXG1 in hPSCs	MGE organoids (FOXG1 syndrome)	Microcephaly, impaired inhibitory interneuron development	[169]
	Electroporation of organoids with shRNA targeting CDK5RAP2	Cerebral organoids (Microcephaly)	Premature neuronal differentiation	[15]
	CRISPR/Cas9-based knock-out of GLB1 in iPSCs	Cerebral organoids (GM1 gangliosidosis)	Accumulation of GM1 ganglioside	[170]
Cancer organoids	Generation of Pdx1-Cre; Kras+/LSL-G12D (KC) and Pdx1-Cre; Kras+/LSL-G12D; Trp53+/LSL-R172H (KPC) mice	Murine pancreatic ductal organoids (pancreatic cancer)	Neoplastic ducts, transcriptional and proteomic changes observed in pancreatic cancers	[232]
	Lentiviral infection for gene transduction, KRASG12V and TP53R175H in pancreatic progenitor cells	Pancreatic progenitor organoids (pancreatic cancer)	Abnormal ductal architecture, neoplastic transformation	[177]
	Isolation of glands from pancreatic cancer patients	Pancreatic cancer organoids	Genomic and transcriptomic alterations in patients, drug response	[176]
	Isolation of glands from gastric cancer patients	Gastric cancer organoids	Aneuploidy, impaired p53 pathway	[178]
	Isolation of tumor tissues from colorectal cancer patients	Colorectal cancer organoids	Genomic and transcriptomic alterations in patients	[179]
	CRISPR/Cas9-based knock-out of APC, SMAD4, and TP53; CRISPR/Cas9-based genome editing (KRASG12V and PIK3CAE545K) in organoids	Colorectal cancer organoids	Tumorigenesis	[189]
	Isolation of circulating tumor cells from prostate cancer patients	Prostate cancer organoids	Phenotypic diversity (AR-dependent/independent), drug response	[180]
	Isolation of tumor tissues from liver cancer patients	Liver cancer organoids	Histological features, expression profiles, tumorigenesis, drug response	[181]
	Isolation of tumor tissues from breast cancer patients	Breast cancer organoids	Histological features, copy number alterations, genomic alterations	[71, 182]
Modeling of other disorders	CRISPR/Cas9-based knock-out of PKD1 or PKD2 in hESCs	Kidney organoids (Polycystic kidney)	Formation of cyst-like structures in tubules	[190]
	CRISPR/Cas9-based genome editing (DKC1-A386T) in iPSCs	Intestinal organoids (Dyskeratosis congenita)	Failure in crypt formation, impaired Wnt signaling, reduced telomere activity	[191]
	CRISPR/Cas9-based genome correction of CFTR-F508del in patient iPSCs	Intestinal organoids (Cystic fibrosis)	Functional repair of CFTR, forskolin-mediated swelling of organoid	[192]
	Lentiviral infection for FUT2 overexpression in human intestinal enteroid	Norovirus-infected intestinal organoids	Susceptible to norovirus replication	[194]