UKAi004-A

General

Cell Line
hPSCreg name	UKAi004-A
Cite as:	UKAi004-A (RRID:CVCL_A5IU)
Alternative name(s)	P4_wt4, patient 1 control 1
Cell line type	Human induced pluripotent stem cell (hiPSC)
Similar lines	UKAi004-B (patient 1 control 2, P4_wt8) Donor's gene variants: KIT, KIT, ABL1, ABL1, ASXL, ASXL, NFE2, NFE2, NRAS, NRAS, TET2, TET2, TET2, TET2, TP53, TP53 Donor diseases: systemic mastocytosis UKAi004-C (P4_mut13, patient 1 D816V 1) Donor's gene variants: KIT, KIT, ABL1, ABL1, ASXL, ASXL, NFE2, NFE2, NRAS, NRAS, TET2, TET2, TET2, TET2, TP53, TP53 Donor diseases: systemic mastocytosis UKAi004-D (P4_mut28, patient 1 D816V 2) Donor's gene variants: KIT, KIT, ABL1, ABL1, ASXL, ASXL, NFE2, NFE2, NRAS, NRAS, TET2, TET2, TET2, TET2, TP53, TP53 Donor diseases: systemic mastocytosis UKAi004-E (P4_mut30, patient 1 D816V 3) Donor's gene variants: KIT, KIT, ABL1, ABL1, ASXL, ASXL, NFE2, NFE2, NRAS, NRAS, TET2, TET2, TET2, TET2, TP53, TP53 Donor diseases: systemic mastocytosis UKAi007-A (P13_wt5, Patient 2 control 1) Donor's gene variants: PDGFRA, PDGFRA, RUNX1, RUNX1, RUNX1, RUNX1, KIT, KIT, ABL1, ABL1, TET2, TET2, TET2, TET2, TET2, TET2, TP53, TP53, ASXL1, ASXL1, IDH1, IDH1, SRSF2, SRSF2 Donor diseases: systemic mastocytosis UKAi007-B (P13_mut1, Patient 2 D816V 1) Donor's gene variants: PDGFRA, PDGFRA, RUNX1, RUNX1, RUNX1, RUNX1, KIT, KIT, ABL1, ABL1, TET2, TET2, TET2, TET2, TET2, TET2, TP53, TP53, ASXL1, ASXL1, IDH1, IDH1, SRSF2, SRSF2 Donor diseases: systemic mastocytosis UKAi008-A (Patient 3 control 1, P15_wt37) Donor's gene variants: PDGFRA, PDGFRA, KIT, KIT, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TP53, TP53, ASXL1, ASXL1 Donor diseases: systemic mastocytosis UKAi008-B (Patient 3 control 2, P15_wt108) Donor's gene variants: PDGFRA, PDGFRA, KIT, KIT, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TP53, TP53, ASXL1, ASXL1 Donor diseases: systemic mastocytosis UKAi008-C (Patient 3 D816V 1, P15_mut131) Donor's gene variants: PDGFRA, PDGFRA, KIT, KIT, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TET2, TP53, TP53, ASXL1, ASXL1 Donor diseases: systemic mastocytosis UKAi001-A (iPS1, hsc3_hiPS_11) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis UKAi001-B (iPS2, hsc3_hiPS_29) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis UKAi001-C (hsc3_hiPS_40, iPS3) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis UKAi001-A-1 (hsc3_hiPS_11_4, IRF8-/- iPS1) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis UKAi001-B-1 (hsc3_hiPS_29_23, IRF8-/- iPS2) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis UKAi001-C-1 (hsc3_hiPS_40_16_6, IRF8-/- iPS3) Donor's gene variants: KRAS, KRAS Donor diseases: systemic mastocytosis
Last update	10th March 2021
Notes	Toledo et al., Blood, ePub ahead of print, 2020 Dec 23
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Provider
Generator	Universitätsklinikum Aachen (UKA) Contact: Universitätsklinikum Aachen (UKA)
Owner	Universitätsklinikum Aachen (UKA)
Distributors	Universitätsklinikum Aachen (UKA)
Derivation country	Germany
External Databases
BioSamples	SAMEA8172007
Cellosaurus	CVCL_A5IU
Wikidata	Q107117221
General Information
Publications	Toledo MAS et al. Nintedanib targets KIT D816V neoplastic cells derived from induced pluripotent stem cells of systemic mastocytosis. Blood. 2021 Apr 15;137(15):2070-2084.
* Is the cell line readily obtainable for third parties?	Yes Research use: allowed Clinical use: not allowed Commercial use: not allowed

Donor Information

General Donor Information

Sex

male

Age of donor (at collection)

60-64

Phenotype and Disease related information (Donor)

Diseases

A disease was diagnosed.

Systemic mastocytosis

Aggressive mastocytosis The donor peripheral blood cells (primary sample) used for reprogramming and iPSC generation are heterogeneous and genetically mosaic. Therefore the five iPSC lines from this donor (UKAi004-A to UKAi004-E) have different allele frequencies than the primary sample for the mutations tested. Please see Table 1 of Toledo et al. 2021 for the allele frequencies of the primary sample and the iPSC lines.

The donor is a carrier of a disease-associated mutation and affected.

Stage

Organs affected: hepatosplenomegaly, lyphnodes, osteoporosis, low platelets

Synonyms

Genetic variants

ABL1 (target)

Chromosome location

9q34.12

Nucleotide sequence variant in HGVS format

c.2972C.T

Protein sequence variant in HGVS format

p.Ser991Leu

Is the variant homozygous or heterozygous?

Heterozygous

ClinVar

NM_007313

ASXL (target)

Chromosome location

20q11.21

Nucleotide sequence variant in HGVS format

c.2444T.C

Protein sequence variant in HGVS format

p.Leu815Pro

Is the variant homozygous or heterozygous?

Homozygous

ClinVar

VCV000013852

NFE2 (target)

Nucleotide sequence variant in HGVS format

c.782_785del

Protein sequence variant in HGVS format

p.Glu261Alafs*3

Is the variant homozygous or heterozygous?

Heterozygous

ClinVar

NM_006163

NRAS (target)

Nucleotide sequence variant in HGVS format

c.35G.A

Protein sequence variant in HGVS format

p.Gly12Asp

Is the variant homozygous or heterozygous?

Heterozygous

ClinVar

NM_002524

TET2 (target)

Chromosome location

4q24

Nucleotide sequence variant in HGVS format

c.2917delT

Protein sequence variant in HGVS format

p.Cys973Alafs*34

Is the variant homozygous or heterozygous?

Heterozygous

ClinVar

NM_001127208

TET2 (target)

Nucleotide sequence variant in HGVS format

c.5284A.G

Protein sequence variant in HGVS format

p.Ile1762Val

Is the variant homozygous or heterozygous?

Homozygous

ClinVar

VCV000135287.1

TP53 (target)

Chromosome location

17p13.1

Nucleotide sequence variant in HGVS format

c.215C.G

Protein sequence variant in HGVS format

p.Pro72Arg

Is the variant homozygous or heterozygous?

Heterozygous

ClinVar

VCV000012351.11

Free text

The donor peripheral blood cells (primary sample) used for reprogramming and iPSC generation are heterogeneous and genetically mosaic. Therefore the five iPSC lines from this donor (UKAi004-A to UKAi004-E) have different allele frequencies than the primary sample for the mutations tested. Please see Table 1 of Toledo et al. 2021 for the allele frequencies of the primary sample and the iPSC lines.

KIT (target)

Chromosome location

4q12

Nucleotide sequence variant in HGVS format

NM_000222.3:c.2447A>T

Protein sequence variant in HGVS format

NP_000213.1:p.Asp816Val

Is the variant homozygous or heterozygous?

Heterozygous

ClinVar

VCV000013852.5

dbSNP

rs121913507

Karyotyping (Donor)

Has the donor karyotype been analysed?

No

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

SAMEA8172012

Ethics

Has informed consent been obtained from the donor of the embryo/tissue from which the pluripotent stem cells have been derived?	Yes
Was the consent voluntarily given?	Yes
Has the donor been informed that participation will not directly influence their personal treatment?	Yes
Can you provide us with a copy of the Donor Information Sheet provided to the donor?	No
Do you (Depositor/Provider) hold the original Donor Consent Form?	No
If you do not hold the Donor Consent Form, do you know who does?	Yes
Alternatives to consent are available?	No
Is there other documentation provided to the donor for consenting purposes?	No
Confirm that consent was obtained by a qualified professional	Yes
Has the donor agreed to be re-contacted?	No
Has the donor been informed about how her/his data will be protected?	Yes
Please indicate whether the data associated with the donated material has been pseudonymised or anonymised.	pseudonymised
Does consent explicitly allow the derivation of pluripotent stem cells?	Yes
* Does consent expressly prevent the derivation of pluripotent stem cells?	No
* Does consent pertain to a specific research project?	No
Does consent permit unforeseen future research, without further consent?	Yes
Does the consent permit uses of donated embryo/tissue or derived cell line intended for clinical treatment or human applications?	No
Does consent expressly prevent development of commercial products?	No
Does consent expressly prevent financial gain from any use of the donated embryo/tissue, including any product made from it?	No
Does consent expressly permit storage of donated embryo/tissue for an unlimited time?	Yes
Does consent expressly permit storage of cells derived from the donated embryo/tissue for an unlimited time?	Yes
Does consent prevent the DONATED BIOSAMPLE from being made available to researchers anywhere in the world?	No
Does consent prevent CELLS DERIVED FROM THE DONATED BIOSAMPLE from being made available to researchers anywhere in the world?	No
Does consent permit research by
an academic institution?	Yes
a public organisation?	Yes
a non-profit company?	Yes
a for-profit corporation?	Yes

Does consent expressly permit collection of genetic information?	Yes
Does consent expressly permit storage of genetic information?	Yes
Does consent prevent dissemination of genetic information?	No
Has the donor been informed that their donated biosample or derived cells may be tested for the presence of microbiological agents / pathogens?	Yes
Has the donor consented to receive information discovered during use of donated embryo/tissue that has significant health implications for the donor?	No
How may genetic information associated with the cell line be accessed?	Controlled Access
Will the donor expect to receive financial benefit, beyond reasonable expenses, in return for donating the biosample?	No
Does the consent anticipate that the donor will be notified of results or outcomes of any research involving the donated samples or derived cells?	No
Does the consent permit the donor, upon withdrawal of consent, to stop the use of the derived cell line(s) that have already been created from donated samples?	Yes
Does the consent permit the donor, upon withdrawal of consent, to stop delivery or use of information and data about the donor?	Yes
Does consent permit access to medical records of the donor?	No
Does consent permit access to any other source of information about the clinical treatment or health of the donor?	No
Has a favourable opinion been obtained from a research ethics committee, or other ethics review panel, in relation to the Research Protocol including the consent provisions?	Yes
Name of accrediting authority involved?	Ethics Commission of Medical Faculty of RWTH Aachen University
Approval number	EK 206/09
Has a favourable opinion been obtained from a research ethics committee, or other ethics review panel, in relation to the PROPOSED PROJECT, involving use of donated embryo/tissue or derived cells?	Yes
Name of accrediting authority involved?	Ethics Commission of Medical Faculty of RWTH Aachen University
Approval number	EK 206/09
Do you have obligations to third parties in regard to the use of the cell line?	No
Are you aware of any further constraints on the use of the donated embryo/tissue or derived cells?	No
Is there an MTA available for the cell line?	Yes
For generation of the cell line, who was the supplier of any recombined DNA vectors or commercial kits used?	Life Technologies
Are you aware of any constraints on the use or distribution of the cell line from the owner or any parties identified in the query above?	No

hIPSC Derivation

General
Source cell type	Peripheral blood Blood circulating throughout the body.
Source cell origin	Peripheral blood Blood circulating throughout the body.
Source cell type (free text)	CD34+ cells (MACS)
Age of donor (at collection)	60-64
Collected in	2015
Passage number reprogrammed	0
Reprogramming method
Vector type	Non-integrating
Vector	Sendai virus
Genes	POU5F1 SOX2 KLF4 MYC
Is reprogramming vector detectable?	Unknown
Vector free reprogramming
Other
Selection criteria for clones	Human ES cell-like morphology
Derived under xeno-free conditions	No
Derived under GMP?	No
Available as clinical grade?	No

Culture Conditions

Surface coating

Gelatin

Feeder cells

mouse embryonic fibroblasts

Passage method

Enzymatically

Collagenase

O2 Concentration

21 %

CO2 Concentration

5 %

Medium

Other medium:

Base medium: Knock out DMEM
Main protein source: Knock-out serum replacement
Serum concentration: 20 %

Supplements

Supplement	Amount	Unit
bFGF	10	ng/ml

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?

Yes

Has Rock inhibitor (Y27632) been used at thaw previously with this cell line?

Yes

Characterisation

Analysis of Undifferentiated Cells

Marker Expression

Marker	Expressed	Immunostaining	RT-PCR	Flow Cytometry	Enzymatic Assay	Expression Profiles
POU5F1 (OCT-4)	Yes
NANOG	Yes
TRA 1-60	Yes
TRA 1-81	Yes

EpiPluriScore

Score: 0,44

Marker	Present	Absent
mCpG	X
OCT4	X

Morphology

Morphology pictures

Differentiation Potency

Endoderm

Endoderm
Ont Id: UBERON_0000925

In vitro spontaneous differentiation

Marker	Expressed
SOX 17	Yes
human albumin	Yes
alpha fetoprotein	Yes
NKX2-5	Yes

Mesoderm

Hematopoietic Precursor Cell
Ont Id: CL_0008001

In vitro spontaneous differentiation

Marker	Expressed
CD34	Yes
MHC6	Yes
CDH5	Yes
T	Yes
CD31	Yes

Ectoderm

Ectoderm
Ont Id: UBERON_0000924

In vitro spontaneous differentiation

Marker	Expressed
Sox1	Yes
GFAP	Yes
PAX6	Yes

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

Genotyping

Karyotyping (Cell Line)
Has the cell line karyotype been analysed?	Yes 46 XY Zellbio_WT_4_II_012_K.TIF Karyotyping method: G-Banding
Other Genotyping (Cell Line)

P4_wt4, patient 1 control 1

General

Cell Line

Provider

External Databases

General Information

Donor Information

General Donor Information

Phenotype and Disease related information (Donor)

ABL1 (target)

ASXL (target)

NFE2 (target)

NRAS (target)

TET2 (target)

TET2 (target)

TP53 (target)

KIT (target)

Karyotyping (Donor)

Other Genotyping (Donor)

Donor Relations

External Databases (Donor)

Ethics

Does consent permit research by

hIPSC Derivation

General

Reprogramming method

Vector free reprogramming

Other

Culture Conditions

Characterisation

Analysis of Undifferentiated Cells

Differentiation Potency

Microbiology / Virus Screening

Genotyping

Karyotyping (Cell Line)

Other Genotyping (Cell Line)