BIONi010-C-6

General

Cell Line
hPSCreg name	BIONi010-C-6
Cite as:	BIONi010-C-6 (RRID:CVCL_II85)
Alternative name(s)	BIONi010-C ApoE E2/E2
Cell line type	Human induced pluripotent stem cell (hiPSC)
Similar lines	BIONi010-C-3 (BIONi010-C ApoE KO #KO30 P30) BIONi010-C-2 (BIONi010-C ApoE E3/E3 #H8 P32) BIONi010-C-4 (BIONi010-C ApoE E4/E4 #B44 P27) UKBi011-A-3 (ApoE 3/3) Donor's gene variants: APOE, APOE Donor diseases: Alzheimer disease UKBi011-A-4 (ApoE 3/4) Donor's gene variants: APOE, APOE Donor diseases: Alzheimer disease UKBi011-A-1 (iLB-AD + ApoE KO) Donor's gene variants: APOE, APOE Donor diseases: Alzheimer disease UKBi011-A-2 (ApoE 2/2) Donor's gene variants: APOE, APOE Donor diseases: Alzheimer disease BIONi010-C (BIONi010-C, K3P53) STBCi006-A-1 (ApoE KO) Donor's gene variants: APOE, APOE Donor diseases: Alzheimer disease STBCi006-A-3 (ApoE 3/3) Donor's gene variants: APOE, APOE Donor diseases: Alzheimer disease STBCi006-A-4 (ApoE 3/4) Donor's gene variants: APOE, APOE Donor diseases: Alzheimer disease UMi042-A-1 (408737 CB9) Donor diseases: Alzheimer's Disease BIONi037-A-2 (BIONi037-A ApoE2/2 #M10-7) BIONi037-A-3 (BIONi037-A ApoE3/4 #P10-22) BIONi037-A-4 (BIONi037-A ApoE4/4 #I10-53) BIONi037-A-1 (16423 ApoE KO) BIONi010-C-25 (BIONi010-C heterozygous TREM2 KO) BIONi010-C-17 (BIONi010-C TREM2 KO) BIONi010-C-70 (BIONi010-C with an APOE 2/2 genotype with an additional, homozygous christchurch mutation) BIONi010-C-71 (BIONi010-C with an APOE 3/3 genotype with an additional, homozygous christchurch mutation) BIONi010-C-72 BIONi010-C-5 (BIONi010-C CD33 E2del #N14 P26) BIONi010-C-7 (BIONi010-C Trem2 R47H) BIONi010-C-8 (BIONi010-C Trem2 T66M, #Y5-80) BIONi010-C-9 (BIONi010-C CD33 KO) BIONi010-C-18 (BIONi010-C TBK1 KO) BIONi010-C-13 (BIONi010-C + NGN2 #I7-26) BIONi010-C-15 (BIONi010-C +dox inducible NGN2-GFP) BIONi010-C-51 (BIONi010-C TNNI3-mCherry reporter) BIONi010-C-19 (BIONi010-C IKBKE KO) BIONi010-C-10 (HNF1AP291fsinsC +/- 54-5) BIONi010-C-11 (HNF1AP291fsinsC -/- 66-1) BIONi010-C-12 (HNF4ApR309C -/- 2-4) BIONi010-C-52 (BIONi010-C with an APOE 2/2 genotype (with two functional alleles in contrast to BIONi010-C-6)) BIONi010-C-53 (BIONi010-C with an APOE 3/3 genotype (with two functional alleles in contrast to BIONi010-C-2)) BIONi010-C-55 (BIONi010-C TNNI3-mCherry/TNNI1-EGFP dual reporter cl. 74) BIONi010-C-24 (BIONi010-C Dox a-syn) BIONi010-C-43 (BIONi010-C + aSNCA-wt AAVS1) BIONi010-C-44 (BIONi010-C + aSNCA-A53T AAVS1) BIONi010-C-54 (BIONi010-C with an APOE 4/4 genotype (with two functional alleles in contrast to BIONi010-C-4)) BIONi010-C-48 (BIONi010-C hMDR1) BIONi010-C-45 (BIONi010-C iCRE AAVS1 GBA1 LoxP EX5-6) BIONi010-C-41 (BIONi010-C + iNGN2 Two-plasmid system/CRISPR-2) BIONi010-C-42 (BIONi010-C + iCRE AAVS1) BIONi010-A (K1P53) BIONi010-B (K2P53, BIONi010-B) UCSFi001-A-74 (FUS-P525L HET 2D1) UCSFi001-A-75 (FUS-P525L HOM 2D2) WTSIi018-B-18 (Kolf 2.1 J (TARDBP M337V WT/SNV)) UQi001-A-1 (C11-TDP43-A382T)
Last update	7th March 2023
Notes	This line is part of a set of isogenic APOE lines based on the iPS cell line BIONi010-C. The set comprises the following APOE genotypes: • BIONi010-C-6 (APOE 2/2) • BIONi010-C-2 (APOE 3/3) • BIONi010-C (APOE 3/4) • BIONi010-C-4 (APOE 4/4) • BIONi010-C-3 (APOE KO) A DNA SNP array revealed no larger chromosomal aberrations to be reported. An unsignificant duplication of 1,4Mbp was found on Chr22 in q11.23. This duplication was found in all isogenic lines generated from BIONi010-C as well as BIONi010-C. Other isogenic ApoE cell line cohorts are also available, generated from BIONi37-A, UKBi011-A and STBci006-A.
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Provider
Generator	Bioneer (BION) Contact: Bioneer (BSC)
Owner	Bioneer (BSC)
Distributors	EBiSC European Collection of Authenticated Cell Cultures (ECACC)
Derivation country	Denmark
External Databases
BioSamples	SAMEA4454009
Cellosaurus	CVCL_II85
Wikidata	Q54796778
General Information
Publications	Schmid B et al. Generation of a set of isogenic, gene-edited iPSC lines homozygous for all main APOE variants and an APOE knock-out line. Stem cell research. 2019 Jan;34:101349. Schmid B et al. Corrigendum to "Generation of a set of isogenic, gene-edited iPSC lines homozygous for all main APOE variants and an APOE knock-out line" [Stem Cell Res. 34/1873-5061 (2019) 101349-55]. Stem cell research. 2020 Oct;48:102005. de Leeuw SM et al. APOE2, E3, and E4 differentially modulate cellular homeostasis, cholesterol metabolism, and inflammatory response in isogenic iPSC-derived astrocytes. Stem cell reports. 2022 Jan 11;17(1):110-126. Somogyi A et al. The synthetic TRPML1 agonist ML-SA1 rescues Alzheimer-related alterations of the endosomal-autophagic-lysosomal system. Journal of cell science. 2023 Mar 15;136(6). Lee H et al. In vitro characterization on the role of APOE polymorphism in human hippocampal neurogenesis. Hippocampus. 2023 Apr;33(4):322-346. Mancuso R et al. Xenografted human microglia display diverse transcriptomic states in response to Alzheimer's disease-related amyloid-β pathology. Nature neuroscience. 2024 May;27(5):886-900.
Projects	ADAPTED: Alzheimer's Disease Apolipoprotein Pathology for Treatment Elucidation and Development EBiSC: European bank of induced pluripotent stem cells
* Is the cell line readily obtainable for third parties?	Yes Research use: allowed Clinical use: not allowed Commercial use: not allowed
Subclone of	BIONi010-C

Donor Information

General Donor Information

Sex

male

Ethnicity

Black or African-American

Phenotype and Disease related information (Donor)

Diseases

No disease was diagnosed.

Disease associated phenotypes

no phenotypes

Other Genotyping (Donor)

Is there genome-wide genotyping or functional data available?

No

Donor Relations

Other cell lines of this donor

External Databases (Donor)

BioSamples

SAMEA3105780

Ethics

Also have a look at the ethics information for the parental line BIONi010-C .

For generation of the cell line, who was the supplier of any recombined DNA vectors or commercial kits used?

hIPSC Derivation

General
The source cell information can be found in the parental cell line BIONi010-C.
Reprogramming method
Vector type	Non-integrating
Vector	Episomal
Genes	POU5F1 SOX2 KLF4 MYC Lin28 shP53
Is reprogramming vector detectable?	No
Vector free reprogramming
Other
Derived under xeno-free conditions	No
Derived under GMP?	No
Available as clinical grade?	No

Culture Conditions

Surface coating	Matrigel/Geltrex
Feeder cells	No
Passage method	Enzyme-free cell dissociation EDTA
O2 Concentration	18 %
CO2 Concentration	5 %
Medium	Essential 8™
Has Rock inhibitor (Y27632) been used at passage previously with this cell line?	Yes
Has Rock inhibitor (Y27632) been used at cryo previously with this cell line?	No
Has Rock inhibitor (Y27632) been used at thaw previously with this cell line?	No

Characterisation

Analysis of Undifferentiated Cells

Morphology

Morphology pictures

Differentiation Potency

Endoderm

Endoderm
Ont Id: UBERON_0000925

In vitro spontaneous differentiation

Marker	Expressed
CXCR4	Yes
PITX1	Yes
GSC	Yes

Mesoderm

Mesoderm
Ont Id: UBERON_0000926

In vitro spontaneous differentiation

Marker	Expressed
NCAM1	Yes
VIM	Yes
DCN	Yes

Ectoderm

Ectoderm
Ont Id: UBERON_0000924

In vitro spontaneous differentiation

Marker	Expressed
NeuroD1	Yes
PAX6	Yes
HES5	Yes

Microbiology / Virus Screening
HIV 1	Negative
HIV 2	Negative
Hepatitis B	Negative
Hepatitis C	Negative
Mycoplasma	Negative

Certificate of Analysis
Is there a certificate of analysis available?	Yes BIONi010-C-6.M001_.CoA_.v1_.pdf Passage: 41

Genotyping

Karyotyping (Cell Line)
Has the cell line karyotype been analysed?	Yes 46 XY Karyotype_ApoE_22.jpg Passage number: 38 Karyotyping method: G-Banding
Other Genotyping (Cell Line)
Is there genome-wide genotyping or functional data available?	Yes Whole genome sequencing https://ega-archive.org/studies/EGAS00001002755 This cell line has undergone WGS using the Illumina HiSeq X platform at 30x coverage. Fastq files are stored at the European Genome Archive, users can apply for access to this data by submitting an application form to the EBiSC Data Access Committee https://ega-archive.org/dacs/EGAC00001000768

Genetic Modification

Disease/phenotype related modifications

Alzheimer disease

Synonyms

Genetic modifications

APOE (target)

Type of modification

Isogenic modification

Chromosome location

19q13.3

Nucleotide sequence variant in HGVS format

NM_000041.4:c.388C>T

Protein sequence variant in HGVS format

NP_000032.1:p.Arg130Cys

Is the modification homozygous or heterozygous?

hemizygous

Free text

BIONi010-C-6 ApoE2/E2 is an isogenic mutant of BIONi010-C (ApoE3/E4). This APOE2/E2 (BIONi010-C-6) line) line has only a single functional APOE allele due to the presence of on-target unintended insertions caused by CRISPR gene editing in one copy of the alleles. BIONi010-C-6 is hemizygous due to a 3.4 kb insertion from the selection plasmid (used during gene editing) in the coding part of one of the two APOE alleles. The remaining (non-disrupted) allele is correctly transcribed and does drive expression of the expected APOE2/E2 isoform. This is characterised in Schmid B, et al. Corrigendum to "Generation of a set of isogenic, gene-edited iPSC lines homozygous for all main APOE variants and an APOE knock-out line". Stem Cell Res. 2020 Oct; 48:102005. doi: 10.1016/j.scr.2020.102005. Jan;34:101349. PMID: 32971461. The genotype at base position described by rs429358 has been modified in the subclone from T/C to T/T, which changes aa from Arg to Cys. Together with other base changes at rs7412 these define a ApoE2/E2 genotype in the subclone. Please see chromatogram for confirmation of the base changes in the subclone.

How has the target locus been modified?

Changed

Available documents

Ran_FA_Nat_Protoc_2013.pdf

BIONi010-C-6.JPG

BIONi010-C-6.jpg
This APOE2/E2 (BIONi010-C-6) line) line has only a single functional APOE allele due to the presence of on-target unintended insertions caused by CRISPR gene editing in one copy of the alleles.

APOE (target)

Type of modification

Isogenic modification

Chromosome location

19q13.3

Nucleotide sequence variant in HGVS format

NM_000041.3:c.526C>T

Protein sequence variant in HGVS format

NP_000032.1:p.Arg176Cys

Is the modification homozygous or heterozygous?

Homozygous

Free text

BIONi010-C-6 ApoE2/E2 is an isogenic mutant of BIONi010-C (ApoE3/E4); The genotype at base position described by rs7412 has been modified in the subclone from C/C to T/T, which changes aa from Arg to Cys. Together with other base changes at rs429358 these define a ApoE2/E2 genotype in the subclone. Please see chromatogram for confirmation of the base changes in the subclone.

How has the target locus been modified?

Changed

BIONi010-C ApoE E2/E2

General

Cell Line

Provider

External Databases

General Information

Donor Information

General Donor Information

Phenotype and Disease related information (Donor)

Other Genotyping (Donor)

Donor Relations

External Databases (Donor)

Ethics

hIPSC Derivation

General

Reprogramming method

Vector free reprogramming

Other

Culture Conditions

Characterisation

Analysis of Undifferentiated Cells

Differentiation Potency

Microbiology / Virus Screening

Certificate of Analysis

Genotyping

Karyotyping (Cell Line)

Other Genotyping (Cell Line)

Genetic Modification

APOE (target)

APOE (target)